Summary

The Debian Med Pure Blend contains 1351 packages which are grouped by metapackages. Each metapackage will cause the installation of packages for a specific topic. The following table lists the metapackages of Debian Med

Tasks page

This is a list of the Tasks Debian Med is made of:

Biology
Biology development
Next generation sequencing
Phylogeny
Cloud
Content management
Covid-19
Medical data
Dental
Epidemiology
Hospital information systems
Imaging
Imaging development
Laboratory
Oncology
Pharmacology
Physics
Practice
Psychology
Rehabilitation
Research
Statistics
Tools
Typesetting

Biology - Debian Med bioinformatics packages

This metapackage will install Debian packages for use in molecular biology, structural biology and other biological sciences.

Official Debian packages with high relevance

Abacas: close gaps in genomic alignments from short reads
Abpoa: adaptive banded Partial Order Alignment
Abyss: de novo, parallel, sequence assembler for short reads
Acedb-other: retrieval of DNA or protein sequences
Adapterremoval: rapid adapter trimming, identification, and read merging of gene sequences
Adun-core: Molecular Simulator
Aegean: integrated genome analysis toolkit
Aevol: digital genetics model to run Evolution Experiments in silico
Alien-hunter: Interpolated Variable Order Motifs to identify horizontally acquired DNA
Alter-sequence-alignment: genomic sequences ALignment Transformation EnviRonment
Altree: program to perform phylogeny-based association and localization analysis
Amap-align: Protein multiple alignment by sequence annealing
Ampliconnoise: removal of noise from 454 sequenced PCR amplicons
Andi: Efficient Estimation of Evolutionary Distances
Anfo: Short Read Aligner/Mapper from MPG
Any2fasta: convert various sequence formats to FASTA
Aragorn: tRNA and tmRNA detection in nucleotide sequences
Arden: specificity control for read alignments using an artificial reference
Ariba: Antibiotic Resistance Identification By Assembly
Art-nextgen-simulation-tools: simulation tools to generate synthetic next-generation sequencing reads
Artemis: genome browser and annotation tool
Artfastqgenerator: outputs artificial FASTQ files derived from a reference genome
Assembly-stats: get assembly statistics from FASTA and FASTQ files
Assemblytics: detect and analyze structural variants from a genome assembly
Atac: genome assembly-to-assembly comparison
Ataqv: ATAC-seq QC and visualization
Atropos: NGS read trimming tool that is specific, sensitive, and speedy
Augur: pipeline components for real-time virus analysis
Augustus: gene prediction in eukaryotic genomes
Autodock: analysis of ligand binding to protein structure
Autodock-vina: docking of small molecules to proteins
Autogrid: pre-calculate binding of ligands to their receptor
Avogadro: Molecular Graphics and Modelling System
Axe-demultiplexer: Trie-based DNA sequencing read demultiplexer
Baitfisher: software package for designing hybrid enrichment probes
Bali-phy: Bayesian Inference of Alignment and Phylogeny
Ballview: free molecular modeling and molecular graphics tool
Bamclipper: Remove gene-specific primer sequences from SAM/BAM alignments
Bamkit: tools for common BAM file manipulations
Bamtools: toolkit for manipulating BAM (genome alignment) files
Bandage: Bioinformatics Application for Navigating De novo Assembly Graphs Easily
Barrnap: rapid ribosomal RNA prediction
Bbmap: BBTools genomic aligner and other tools for short sequences
Bcalm: de Bruijn compaction in low memory
Bcftools: genomic variant calling and manipulation of VCF/BCF files
Beads: 2-DE electrophoresis gel image spot detection
Beagle: Genotype calling, genotype phasing and imputation of ungenotyped markers
Beast-mcmc: Bayesian MCMC phylogenetic inference
Beast2-mcmc: Bayesian MCMC phylogenetic inference
Bedops: high-performance genomic feature operations
Bedtools: suite of utilities for comparing genomic features
Belvu: multiple sequence alignment viewer and phylogenetic tool
Berkeley-express: Streaming quantification for high-throughput sequencing
Bifrost: parallel construction, indexing and querying of de Bruijn graphs
Bio-eagle: Haplotype phasing within a genotyped cohort or using a phased reference panel
Bio-rainbow: clustering and assembling short reads for bioinformatics
Bio-tradis: analyse the output from TraDIS analyses of genomic sequences
Bio-vcf: domain specific language (DSL) for processing the VCF format
Bioawk: extension of awk for biological sequence analysis
Biobambam2: tools for early stage alignment file processing
Biosyntax: Syntax Highlighting for Computational Biology (metapackage)
Bitseq: Bayesian Inference of Transcripts from Sequencing Data
Blasr: mapping single-molecule sequencing reads
Blixem: interactive browser of sequence alignments
Bolt-lmm: Efficient large cohorts genome-wide Bayesian mixed-model association testing
Bowtie: Ultrafast memory-efficient short read aligner
Bowtie2: ultrafast memory-efficient short read aligner
Boxshade: Pretty-printing of multiple sequence alignments
Bppphyview: Bio++ Phylogenetic Viewer
Bppsuite: Bio++ program suite
Brig: BLAST Ring Image Generator
Btllib-tools: Bioinformatics Technology Lab common code library tools
Busco: benchmarking sets of universal single-copy orthologs
Bustools: program for manipulating BUS files for single cell RNA-Seq datasets
Bwa: Burrows-Wheeler Aligner
Canu: single molecule sequence assembler for genomes
Cassiopee: index and search tool in genomic sequences
Cat-bat: taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Cct: visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
Cd-hit: suite of programs designed to quickly group sequences
Cdbfasta: Constant DataBase indexing and retrieval tools for multi-FASTA files
Centrifuge: rapid and memory-efficient system for classification of DNA sequences
Cgview: Circular Genome Viewer
Changeo: Repertoire clonal assignment toolkit (Python 3)
Chimeraslayer: detects likely chimeras in PCR amplified DNA
Chromhmm: Chromatin state discovery and characterization
Chromimpute: Large-scale systematic epigenome imputation
Cif-tools: Suite of tools to manipulate, validate and query mmCIF files
Circlator: circularize genome assemblies
Circos: plotter for visualizing data
Clearcut: extremely efficient phylogenetic tree reconstruction
Clonalframe: inference of bacterial microevolution using multilocus sequence data
Clonalframeml: Efficient Inference of Recombination in Whole Bacterial Genomes
Clonalorigin: inference of homologous recombination in bacteria using whole genome sequences
Clustalo: General-purpose multiple sequence alignment program for proteins
Clustalw: global multiple nucleotide or peptide sequence alignment
Clustalx: Multiple alignment of nucleic acid and protein sequences (graphical interface)
Cnvkit: Copy number variant detection from targeted DNA sequencing
Codonw: Correspondence Analysis of Codon Usage
Comet-ms: Tandem mass spectrometry (MS/MS) search engine
Concavity: predictor of protein ligand binding sites from structure and conservation
Conservation-code: protein sequence conservation scoring tool
Covtobed: convert the coverage track from a BAM file into a BED file
Crac: integrated RNA-Seq read analysis
Csb: Computational Structural Biology Toolbox (CSB)
Ctffind: fast and accurate defocus estimation from electron micrographs
Cutadapt: Clean biological sequences from high-throughput sequencing reads
Cutesv: comprehensive discovery of structural variations of genomic sequences
Daligner: local alignment discovery between long nucleotide sequencing reads
Damapper: long read to reference genome mapping tool
Datamash: statistics tool for command-line interface
Dawg: simulate the evolution of recombinant DNA sequences
Dazzdb: manage nucleotide sequencing read data
Deblur: deconvolution for Illumina amplicon sequencing
Deepnano: alternative basecaller for MinION reads of genomic sequences
Delly: Structural variant discovery by read analysis
Density-fitness: Calculates per-residue electron density scores
Dextractor: (d)extractor and compression command library
Dialign: Segment-based multiple sequence alignment
Dialign-tx: Segment-based multiple sequence alignment
Diamond-aligner: accelerated BLAST compatible local sequence aligner
Discosnp: discovering Single Nucleotide Polymorphism from raw set(s) of reads
Disulfinder: cysteines disulfide bonding state and connectivity predictor
Dnaclust: tool for clustering millions of short DNA sequences
Dnarrange: Method to find rearrangements in long DNA reads relative to a genome seq
Dotter: detailed comparison of two genomic sequences
Drop-seq-tools: analyzing Drop-seq data
Dssp: protein secondary structure assignment based on 3D structure
Dwgsim: short sequencing read simulator
E-mem: Efficient computation of Maximal Exact Matches for very large genomes
Ea-utils: command-line tools for processing biological sequencing data
Ecopcr: estimate PCR barcode primers quality
Edtsurf: triangulated mesh surfaces for protein structures
Eigensoft: reduction of population bias for genetic analyses
Elph: DNA/protein sequence motif finder
Embassy-domainatrix: Extra EMBOSS commands to handle domain classification file
Embassy-domalign: Extra EMBOSS commands for protein domain alignment
Embassy-domsearch: Extra EMBOSS commands to search for protein domains
Emboss: European molecular biology open software suite
Emmax: genetic mapping considering population structure
Estscan: ORF-independent detector of coding DNA sequences
Examl: Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
Exonerate: generic tool for pairwise sequence comparison
Fasta3: tools for searching collections of biological sequences
Fastahack: utility for indexing and sequence extraction from FASTA files
Fastani: Fast alignment-free computation of whole-genome Average Nucleotide Identity
Fastaq: FASTA and FASTQ file manipulation tools
Fastdnaml: Tool for construction of phylogenetic trees of DNA sequences
Fastlink: faster version of pedigree programs of Linkage
Fastml: maximum likelihood ancestral amino-acid sequence reconstruction
Fastp: Ultra-fast all-in-one FASTQ preprocessor
Fastq-pair: Rewrites paired end fastq so all reads have a mate to separate out singletons
Fastqc: quality control for high throughput sequence data
Fastqtl: Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes
Fasttree: phylogenetic trees from alignments of nucleotide or protein sequences
Ffindex: simple index/database for huge amounts of small files
Figtree: graphical phylogenetic tree viewer
Filtlong: quality filtering tool for long reads of genome sequences
Fitgcp: fitting genome coverage distributions with mixture models
Flash: Fast Length Adjustment of SHort reads
Flexbar: flexible barcode and adapter removal for sequencing platforms
Flye: de novo assembler for single molecule sequencing reads using repeat graphs
Fml-asm: tool for assembling Illumina short reads in small regions
Freebayes: Bayesian haplotype-based polymorphism discovery and genotyping
Freecontact: fast protein contact predictor
Fsa: Fast Statistical Alignment of protein, RNA or DNA sequences
Fsm-lite: frequency-based string mining (lite)
Gamgi: General Atomistic Modelling Graphic Interface (GAMGI)
Garli: phylogenetic analysis of molecular sequence data using maximum-likelihood
Garlic: visualization program for biomolecules
Gasic: genome abundance similarity correction
Gatb-core: Genome Analysis Toolbox with de-Bruijn graph
Gbrowse: GMOD Generic Genome Browser
Gdpc: visualiser of molecular dynamic simulations
Gemma: Genome-wide Efficient Mixed Model Association
Genometester: toolkit for performing set operations on k-mer lists
Genomethreader: software tool to compute gene structure predictions
Genometools: versatile genome analysis toolkit
Genomicsdb-tools: sparse array storage library for genomics (tools)
Gentle: suite to plan genetic cloning
Gff2aplot: pair-wise alignment-plots for genomic sequences in PostScript
Gff2ps: produces PostScript graphical output from GFF-files
Gffread: GFF/GTF format conversions, region filtering, FASTA sequence extraction
Ggd-utils: programs for use in ggd
Ghemical: GNOME molecular modelling environment
Ghmm: General Hidden-Markov-Model library - tools
Glam2: gapped protein motifs from unaligned sequences
Gmap: spliced and SNP-tolerant alignment for mRNA and short reads
Grabix: wee tool for random access into BGZF files
Graphlan: circular representations of taxonomic and phylogenetic trees
Grinder: Versatile omics shotgun and amplicon sequencing read simulator
Gromacs: Molecular dynamics simulator, with building and analysis tools
Gsort: sort genomic data
Gubbins: phylogenetic analysis of genome sequences
Gwama: Genome-Wide Association Meta Analysis
Harvest-tools: archiving and postprocessing for reference-compressed genomic multi-alignments
Hhsuite: sensitive protein sequence searching based on HMM-HMM alignment
Hilive: realtime alignment of Illumina reads
Hisat2: graph-based alignment of short nucleotide reads to many genomes
Hmmer: profile hidden Markov models for protein sequence analysis
Hmmer2: profile hidden Markov models for protein sequence analysis
Hyphy-mpi: Hypothesis testing using Phylogenies (MPI version)
Hyphy-pt: Hypothesis testing using Phylogenies (pthreads version)
Idba: iterative De Bruijn Graph short read assemblers
Igblast: Immunoglobulin and T cell receptor variable domain sequence analysis
Igdiscover: analyzes antibody repertoires to find new V genes
Igor: infers V(D)J recombination processes from sequencing data
Igv: Integrative Genomics Viewer
Indelible: powerful and flexible simulator of biological evolution
Infernal: inference of RNA secondary structural alignments
Insilicoseq: sequencing simulator producing realistic Illumina reads
Ipig: integrating PSMs into genome browser visualisations
Iqtree: efficient phylogenetic software by maximum likelihood
Iva: iterative virus sequence assembler
Jaligner: Smith-Waterman algorithm with Gotoh's improvement
Jalview: multiple alignment editor
Jellyfish: count k-mers in DNA sequences
Jellyfish1: count k-mers in DNA sequences
Jmodeltest: HPC selection of models of nucleotide substitution
Jmol: Molecular Viewer
Kalign: Global and progressive multiple sequence alignment
Kallisto: near-optimal RNA-Seq quantification
Kaptive: obtain information about K and O types for Klebsiella genome assemblies
Khmer: in-memory DNA sequence kmer counting, filtering & graph traversal
Kineticstools: detection of DNA modifications
King-probe: Evaluate and visualize protein interatomic packing
Kissplice: Detection of various kinds of polymorphisms in RNA-seq data
Kleborate: tool to screen Klebsiella genome assemblies
Kma: mapping genomic sequences to raw reads directly against redundant databases
Kmc: count kmers in genomic sequences
Kmer: suite of tools for DNA sequence analysis
Kmerresistance: correlates mapped genes with the predicted species of WGS samples
Kraken: assigning taxonomic labels to short DNA sequences
Kraken2: taxonomic classification system using exact k-mer matches
Lagan: highly parametrizable pairwise global genome sequence aligner
Lamarc: Likelihood Analysis with Metropolis Algorithm using Random Coalescence
Lamassemble: Merges overlapping "long" DNA reads into a consensus sequences
Lambda-align: Local Aligner for Massive Biological DatA
Lambda-align2: Local Aligner for Massive Biological DatA - v2
Last-align: genome-scale comparison of biological sequences
Lastz: pairwise aligning DNA sequences
Leaff: biological sequence library utilities and applications
Lefse: determine features of organisms, clades, taxonomic units, genes
Libpwiz-tools: ProteoWizard command line tools
Librg-utils-perl: parsers and format conversion utilities used by (e.g.) profphd
Libvcflib-tools: C++ library for parsing and manipulating VCF files (tools)
Lighter: fast and memory-efficient sequencing error corrector
Logol: ??? missing short description for package logol :-(
Loki: MCMC linkage analysis on general pedigrees
Ltrsift: postprocessing and classification of LTR retrotransposons
Lucy: DNA sequence quality and vector trimming tool
Lumpy-sv: general probabilistic framework for structural variant discovery
Macs: Model-based Analysis of ChIP-Seq on short reads sequencers
Macsyfinder: detection of macromolecular systems in protein datasets
Maffilter: process genome alignment in the Multiple Alignment Format
Mafft: Multiple alignment program for amino acid or nucleotide sequences
Malt: sequence alignment and analysis tool to process sequencing data
Mapdamage: tracking and quantifying damage patterns in ancient DNA sequences
Mapsembler2: bioinformatics targeted assembly software
Maq: maps short fixed-length polymorphic DNA sequence reads to reference sequences
Maqview: graphical read alignment viewer for short gene sequences
Mash: fast genome and metagenome distance estimation using MinHash
Massxpert: transitional package for massxpert -> massxpert2
Mauve-aligner: multiple genome alignment
Mcaller: find methylation in nanopore reads
Mecat2: ultra-fast and accurate de novo assembly tools for SMRT reads
Megadepth: computes coverage from BigWig and BAM sequencing files
Megahit: ultra-fast and memory-efficient meta-genome assembler
Megan-ce: interactive tool to explore and analyse microbiome sequencing data
Melting: compute the melting temperature of nucleic acid duplex
Meryl: in- and out-of-core kmer counting and utilities
Metabat: robust statistical framework for reconstructing genomes from metagenomic data
Metaeuk: sensitive, high-throughput gene discovery and annotation for metagenomics
Metaphlan: Metagenomic Phylogenetic Analysis
Metastudent: predictor of Gene Ontology terms from protein sequence
Mhap: locality-sensitive hashing to detect long-read overlaps
Microbegps: explorative taxonomic profiling tool for metagenomic data
Microbiomeutil: Microbiome Analysis Utilities
Mindthegap: performs detection and assembly of DNA insertion variants in NGS read datasets
Minexpert2: MS^n mass spectrometric data visualization and mining (runtime)
Minia: short-read biological sequence assembler
Miniasm: ultrafast de novo assembler for long noisy DNA sequencing reads
Minimac4: Fast Imputation Based on State Space Reduction HMM
Minimap: tool for approximate mapping of long biosequences such as DNA reads
Minimap2: versatile pairwise aligner for genomic and spliced nucleotide sequences
Mipe: Tools to store PCR-derived data
Mira-assembler: Whole Genome Shotgun and EST Sequence Assembler
Mirtop: annotate miRNAs with a standard mirna/isomir naming
Mlv-smile: Find statistically significant patterns in sequences
Mmb: model the structure and dynamics of macromolecules
Mmseqs2: ultra fast and sensitive protein search and clustering
Mosdepth: BAM/CRAM depth calculation biological sequencing
Mothur: sequence analysis suite for research on microbiota
Mptp: single-locus species delimitation
Mrbayes: Bayesian Inference of Phylogeny
Multiqc: output integration for RNA sequencing across tools and samples
Mummer: Efficient sequence alignment of full genomes
Murasaki: homology detection tool across multiple large genomes
Murasaki-mpi: homology detection tool across multiple large genomes (MPI-version)
Muscle: Multiple alignment program of protein sequences
Muscle3: multiple alignment program of protein sequences
Mustang: multiple structural alignment of proteins
Nanofilt: filtering and trimming of long read sequencing data
Nanolyse: remove lambda phage reads from a fastq file
Nanook: pre- and post-alignment analysis of nanopore sequencing data
Nanopolish: consensus caller for nanopore sequencing data
Nanostat: statistics on long biological sequences
Nanosv: structural variant caller for nanopore data
Nast-ier: NAST-based DNA alignment tool
Ncbi-acc-download: download genome files from NCBI by accession
Ncbi-blast+: next generation suite of BLAST sequence search tools
Ncbi-blast+-legacy: NCBI Blast legacy call script
Ncbi-entrez-direct: NCBI Entrez utilities on the command line
Ncbi-epcr: Tool to test a DNA sequence for the presence of sequence tagged sites
Ncbi-seg: tool to mask segments of low compositional complexity in amino acid sequences
Ncbi-tools-bin: NCBI libraries for biology applications (text-based utilities)
Ncbi-tools-x11: NCBI libraries for biology applications (X-based utilities)
Ncl-tools: tools to deal with NEXUS files
Ncoils: coiled coil secondary structure prediction
Neobio: computes alignments of amino acid and nucleotide sequences
Ngmlr: CoNvex Gap-cost alignMents for Long Reads
Njplot: phylogenetic tree drawing program
Norsnet: tool to identify unstructured loops in proteins
Norsp: predictor of non-regular secondary structure
Ntcard: Streaming algorithm to estimate cardinality in genomics datasets
Nxtrim: Optimized trimming of Illumina mate pair reads
Obitools: programs to analyze NGS data in a DNA metabarcoding context
Openms: package for LC/MS data management and analysis
Optimir: Integrating genetic variations in miRNA alignment
Pal2nal: converts proteins to genomic DNA alignment
Paleomix: pipelines and tools for the processing of ancient and modern HTS data
Paml: Phylogenetic Analysis by Maximum Likelihood (PAML)
Paraclu: Parametric clustering of genomic and transcriptomic features
Parasail: Aligner based on libparasail
Parsinsert: Parsimonious Insertion of unclassified sequences into phylogenetic trees
Parsnp: rapid core genome multi-alignment
Patman: rapid alignment of short sequences to large databases
Pbdagcon: sequence consensus using directed acyclic graphs
Pbhoney: genomic structural variation discovery
Pbjelly: genome assembly upgrading tool
Pbsim: simulator for PacBio sequencing reads
Pbsuite: software for Pacific Biosciences sequencing data
Pdb2pqr: Preparation of protein structures for electrostatics calculations
Perlprimer: Graphical design of primers for PCR
Perm: efficient mapping of short reads with periodic spaced seeds
Pftools: build and search protein and DNA generalized profiles
Phast: phylogenetic analysis with space/time models
Phipack: PHI test and other tests of recombination
Phybin: binning/clustering newick trees by topology
Phylip: package of programs for inferring phylogenies
Phylonium: Fast and Accurate Estimation of Evolutionary Distances
Phyml: Phylogenetic estimation using Maximum Likelihood
Physamp: sample sequence alignment corresponding to phylogeny
Phyutility: simple analyses or modifications on both phylogenetic trees and data matrices
Phyx: UNIX-style phylogenetic analyses on trees and sequences
Picard-tools: Command line tools to manipulate SAM and BAM files
Picopore: lossless compression of Nanopore files
Pigx-rnaseq: pipeline for checkpointed and distributed RNA-seq analyses
Piler: genomic repeat analysis
Pilercr: software for finding CRISPR repeats
Pilon: automated genome assembly improvement and variant detection tool
Pinfish: Collection of tools to annotate genomes using long read transcriptomics data
Pique: software pipeline for performing genome wide association studies
Pirs: Profile based Illumina pair-end Reads Simulator
Pizzly: Identifies gene fusions in RNA sequencing data
Placnet: Plasmid Constellation Network project
Plasmidid: mapping-based, assembly-assisted plasmid identification tool
Plasmidomics: draw plasmids and vector maps with PostScript graphics export
Plasmidseeker: identification of known plasmids from whole-genome sequencing reads
Plast: Parallel Local Sequence Alignment Search Tool
Plink: whole-genome association analysis toolset
Plink1.9: whole-genome association analysis toolset
Plink2: whole-genome association analysis toolset
Plip: fully automated protein-ligand interaction profiler
Poa: Partial Order Alignment for multiple sequence alignment
Populations: population genetic software
Porechop: adapter trimmer for Oxford Nanopore reads
Poretools: toolkit for nanopore nucleotide sequencing data
Pplacer: phylogenetic placement and downstream analysis
Prank: Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
Predictnls: prediction and analysis of protein nuclear localization signals
Presto: toolkit for processing B and T cell sequences
Prime-phylo: bayesian estimation of gene trees taking the species tree into account
Primer3: tool to design flanking oligo nucleotides for DNA amplification
Prinseq-lite: PReprocessing and INformation of SEQuence data (lite version)
Proalign: Probabilistic multiple alignment program
Probabel: Toolset for Genome-Wide Association Analysis
Probalign: multiple sequence alignment using partition function posterior probabilities
Probcons: PROBabilistic CONSistency-based multiple sequence alignment
Proda: multiple alignment of protein sequences
Prodigal: Microbial (bacterial and archaeal) gene finding program
Profbval: predictor of flexible/rigid protein residues from sequence
Profisis: prediction of protein-protein interaction sites from sequence
Profnet-bval: neural network architecture for profbval
Profnet-chop: neural network architecture for profchop
Profnet-con: neural network architecture for profcon
Profnet-isis: neural network architecture for profisis
Profnet-md: neural network architecture for metadisorder
Profnet-norsnet: neural network architecture for norsnet
Profnet-prof: neural network architecture for profacc
Profnet-snapfun: neural network architecture for snapfun
Profphd: secondary structure and solvent accessibility predictor
Profphd-net: neural network architecture for profphd
Profphd-utils: profphd helper utilities convert_seq and filter_hssp
Proftmb: per-residue prediction of bacterial transmembrane beta barrels
Progressivemauve: multiple genome alignment algorithms
Prokka: rapid annotation of prokaryotic genomes
Proteinortho: Detection of (Co-)orthologs in large-scale protein analysis
Prottest: selection of best-fit models of protein evolution
Provean: Protein Variation Effect Analyzer
Pscan-chip: ChIP-based identifcation of TF binding sites
Pscan-tfbs: search for transcription factor binding sites
Psortb: bacterial localization prediction tool
Pullseq: Extract sequence from a fasta or fastq
Pycoqc: computes metrics and generates Interactive QC plots
Pycorrfit: tool for fitting correlation curves on a logarithmic plot
Pyensembl: installs data from the Ensembl genome database
Pyfastx: fast random access to sequences from FASTA/Q file - command
Pymol: Molecular Graphics System
Pyscanfcs: scientific tool for perpendicular line scanning FCS
Python3-biomaj3-daemon: BioMAJ daemon library
Python3-bioxtasraw: process biological small angle scattering data
Python3-cogent3: framework for genomic biology
Python3-emperor: visualizing high-throughput microbial community data
Python3-geneimpacts: wraps command line tools to assess variants in gene sequences
Python3-gffutils: Work with GFF and GTF files in a flexible database framework
Python3-pairtools: Framework to process sequencing data from a Hi-C experiment
Python3-pybedtools: Python 3 wrapper around BEDTools for bioinformatics work
Python3-sqt: SeQuencing Tools for biological DNA/RNA high-throughput data
Python3-treetime: inference of time stamped phylogenies and ancestral reconstruction (Python 3)
Pyvcf: helper scripts for Variant Call Format (VCF) parser
Qcat: demultiplexing Oxford Nanopore reads from FASTQ files
Qcumber: quality control of genomic sequences
Qiime: Quantitative Insights Into Microbial Ecology
Qtltools: Tool set for molecular QTL discovery and analysis
Quicktree: Neighbor-Joining algorithm for phylogenies
Quorum: QUality Optimized Reads of genomic sequences
Qutemol: interactive visualization of macromolecules
R-bioc-annotate: BioConductor annotation for microarrays
R-bioc-biostrings: GNU R string objects representing biological sequences
R-bioc-bitseq: transcript expression inference and analysis for RNA-seq data
R-bioc-cner: CNE Detection and Visualization
R-bioc-cummerbund: tool for analysis of Cufflinks RNA-Seq output
R-bioc-deseq2: R package for RNA-Seq Differential Expression Analysis
R-bioc-ebseq: R package for RNA-Seq Differential Expression Analysis
R-bioc-edger: Empirical analysis of digital gene expression data in R
R-bioc-genefilter: methods for filtering genes from microarray experiments
R-bioc-geoquery: Get data from NCBI Gene Expression Omnibus (GEO)
R-bioc-hilbertvis: GNU R package to visualise long vector data
R-bioc-htsfilter: GNU R filter replicated high-throughput transcriptome sequencing data
R-bioc-impute: Imputation for microarray data
R-bioc-limma: linear models for microarray data
R-bioc-megadepth: BioCOnductor BigWig and BAM related utilities
R-bioc-mergeomics: Integrative network analysis of omics data
R-bioc-metagenomeseq: GNU R statistical analysis for sparse high-throughput sequencing
R-bioc-mofa: Multi-Omics Factor Analysis (MOFA)
R-bioc-multiassayexperiment: Software for integrating multi-omics experiments in BioConductor
R-bioc-mutationalpatterns: GNU R comprehensive genome-wide analysis of mutational processes
R-bioc-phyloseq: GNU R handling and analysis of high-throughput microbiome census data
R-bioc-rtracklayer: GNU R interface to genome browsers and their annotation tracks
R-bioc-scater: Single-Cell Analysis Toolkit for Gene Expression Data in R
R-bioc-tfbstools: GNU R Transcription Factor Binding Site (TFBS) Analysis
R-cran-adegenet: GNU R exploratory analysis of genetic and genomic data
R-cran-adephylo: GNU R exploratory analyses for the phylogenetic comparative method
R-cran-alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis
R-cran-ape: GNU R package for Analyses of Phylogenetics and Evolution
R-cran-bio3d: GNU R package for biological structure analysis
R-cran-distory: GNU R distance between phylogenetic histories
R-cran-genabel: GNU R package for genome-wide SNP association analysis
R-cran-kaos: Encoding of Sequences Based on Frequency Matrix Chaos
R-cran-metamix: GNU R bayesian mixture analysis for metagenomic community profiling
R-cran-phangorn: GNU R package for phylogenetic analysis
R-cran-phytools: GNU R phylogenetic tools for comparative biology
R-cran-pscbs: R package: Analysis of Parent-Specific DNA Copy Numbers
R-cran-qtl: GNU R package for genetic marker linkage analysis
R-cran-rotl: GNU R interface to the 'Open Tree of Life' API
R-cran-samr: GNU R significance analysis of microarrays
R-cran-sdmtools: Species Distribution Modelling Tools
R-cran-seqinr: GNU R biological sequences retrieval and analysis
R-cran-seurat: Tools for Single Cell Genomics
R-cran-shazam: Immunoglobulin Somatic Hypermutation Analysis
R-cran-spp: GNU R ChIP-seq processing pipeline
R-cran-tcr: Advanced Data Analysis of Immune Receptor Repertoires
R-cran-tigger: Infers new Immunoglobulin alleles from Rep-Seq Data
R-cran-treespace: Statistical Exploration of Landscapes of Phylogenetic Trees
R-cran-tsne: t-distributed stochastic neighbor embedding for R (t-SNE)
R-cran-vegan: Community Ecology Package for R
R-cran-webgestaltr: find over-represented properties in gene lists
R-cran-wgcna: Weighted Correlation Network Analysis
R-other-ascat: Allele-Specific Copy Number Analysis of Tumours
R-other-mott-happy.hbrem: GNU R package for fine-mapping complex diseases
R-other-rajewsky-dropbead: Basic Exploration and Analysis of Drop-seq Data
Racon: consensus module for raw de novo DNA assembly of long uncorrected reads
Radiant: explore hierarchical metagenomic data with zoomable pie charts
Ragout: Reference-Assisted Genome Ordering UTility
Rambo-k: Read Assignment Method Based On K-mers
Rampler: module for sampling genomic sequences
Rapmap: rapid sensitive and accurate DNA read mapping via quasi-mapping
Rasmol: visualization of biological macromolecules
Raster3d: tools for generating images of proteins or other molecules
Rate4site: detector of conserved amino-acid sites
Raxml: Randomized Axelerated Maximum Likelihood of phylogenetic trees
Ray: de novo genome assemblies of next-gen sequencing data
Rdp-alignment: Ribosomal Database Project (RDP) alignment tools package
Rdp-classifier: extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
Rdp-readseq: Ribosomal Database Project (RDP) sequence reading and writing
Readseq: Conversion between sequence formats
Readucks: Nanopore read de-multiplexer (read demux -> readux -> readucks, innit)
Reapr: universal tool for genome assembly evaluation
Recan: genetic distance plotting for recombination events analysis
Relion: toolkit for 3D reconstructions in cryo-electron microscopy
Relion-gui: toolkit for 3D reconstructions in cryo-electron microscopy (gui apps)
Repeatmasker-recon: finds repeat families from biological sequences
Reprof: protein secondary structure and accessibility predictor
Resfinder: identify acquired antimicrobial resistance genes
Rna-star: ultrafast universal RNA-seq aligner
Rnahybrid: Fast and effective prediction of microRNA/target duplexes
Roary: high speed stand alone pan genome pipeline
Rockhopper: system for analyzing bacterial RNA-seq data
Roguenarok: versatile and scalable algorithm for rogue taxon identification
Rsem: RNA-Seq by Expectation-Maximization
Rtax: Classification of sequence reads of 16S ribosomal RNA gene
Runcircos-gui: GUI tool to run circos
Saint: Significance Analysis of INTeractome
Salmid: rapid Kmer based Salmonella identifier from sequence data
Salmon: wicked-fast transcript quantification from RNA-seq data
Sambamba: tools for working with SAM/BAM data
Samblaster: marks duplicates, extracts discordant/split reads
Samclip: filter SAM file for soft and hard clipped alignments
Samtools: processing sequence alignments in SAM, BAM and CRAM formats
Savvy-util: conversion tool for SAV file format
Scoary: pangenome-wide association studies
Scrappie: basecaller for Nanopore sequencer
Scrm: simulator of evolution of genetic sequences
Scythe: Bayesian adaptor trimmer for sequencing reads
Seaview: Multiplatform interface for sequence alignment and phylogeny
Seer: genomic sequence element (kmer) enrichment analysis
Segemehl: short read mapping with gaps
Sepp: phylogeny with ensembles of Hidden Markov Models
Seqan-apps: C++ library for the analysis of biological sequences
Seqan-needle: pre-filter for the counting of very large collections of nucleotide sequences
Seqan-raptor: pre-filter for querying very large collections of nucleotide sequences
Seqkit: cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Seqmagick: imagemagick-like frontend to Biopython SeqIO
Seqprep: stripping adaptors and/or merging paired reads of DNA sequences with overlap
Seqsero: Salmonella serotyping from genome sequencing data
Seqtk: Fast and lightweight tool for processing sequences in the FASTA or FASTQ format
Sga: de novo genome assembler that uses string graphs
Shasta: nanopore whole genome assembly (binaries and scripts)
Shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
Sibelia: comparative genomics tool
Sibsim4: align expressed RNA sequences on a DNA template
Sickle: windowed adaptive trimming tool for FASTQ files using quality
Sigma-align: Simple greedy multiple alignment of non-coding DNA sequences
Sim4: tool for aligning cDNA and genomic DNA
Sim4db: batch spliced alignment of cDNA sequences to a target genome
Simka: comparative metagenomics method dedicated to NGS datasets
Simkamin: approximate comparative metagenomics method dedicated to NGS datasets
Ska: Split Kmer Analysis
Skesa: strategic Kmer extension for scrupulous assemblies
Skewer: post-processing of high-throughput DNA sequence reads
Smalt: Sequence Mapping and Alignment Tool
Smithwaterman: determine similar regions between two strings or genomic sequences
Smrtanalysis: software suite for single molecule, real-time sequencing
Snap: location of genes from DNA sequence with hidden markov model
Snap-aligner: Scalable Nucleotide Alignment Program
Sniffles: structural variation caller using third-generation sequencing
Snippy: rapid haploid variant calling and core genome alignment
Snp-sites: Binary code for the package snp-sites
Snpeff: genetic variant annotation and effect prediction toolbox - tool
Snpomatic: fast, stringent short-read mapping software
Snpsift: tool to annotate and manipulate genome variants - tool
Soapaligner: aligner of short reads of next generation sequencers
Soapdenovo: short-read assembly method to build de novo draft assembly
Soapdenovo2: short-read assembly method to build de novo draft assembly
Soapsnp: resequencing utility that can assemble consensus sequence of genomes
Sortmerna: tool for filtering, mapping and OTU-picking NGS reads
Spaced: alignment-free sequence comparison using spaced words
Spades: genome assembler for single-cell and isolates data sets
Spaln: splicing-aware transcript-alignment to genomic DNA
Spoa: SIMD partial order alignment tool
Sprai: single-pass sequencing read accuracy improver
Spread-phy: analyze and visualize phylogeographic reconstructions
Squizz: Converter for genetic sequences and alignments
Sra-toolkit: utilities for the NCBI Sequence Read Archive
Srst2: Short Read Sequence Typing for Bacterial Pathogens
Ssake: genomics application for assembling millions of very short DNA sequences
Sspace: scaffolding pre-assembled contigs after extension
Ssw-align: Smith-Waterman aligner based on libssw
Stacks: pipeline for building loci from short-read DNA sequences
Staden: DNA sequence assembly (Gap4/Gap5), editing and analysis tools
Staden-io-lib-utils: programs for manipulating DNA sequencing files
Stringtie: assemble short RNAseq reads to transcripts
Subread: toolkit for processing next-gen sequencing data
Suitename: categorize each suite in an RNA backbone
Sumaclust: fast and exact clustering of genomic sequences
Sumatra: fast and exact comparison and clustering of sequences
Sumtrees: Phylogenetic Tree Summarization and Annotation
Surankco: Supervised Ranking of Contigs in de novo Assemblies
Surpyvor: modification of VCF files with SURVIVOR
Survivor: tool set for simulating/evaluating SVs
Svim: Structural variant caller for long sequencing reads
Swarm: robust and fast clustering method for amplicon-based studies
Sweed: assessment of SNPs for their evolutionary advantage
T-coffee: Multiple Sequence Alignment
Tabix: generic indexer for TAB-delimited genome position files
Tantan: low complexity and tandem repeat masker for biosequences
Terraphast: enumerate terraces in phylogenetic tree space
Theseus: superimpose macromolecules using maximum likelihood
Thesias: Testing Haplotype Effects In Association Studies
Tiddit: structural variant calling
Tigr-glimmer: Gene detection in archea and bacteria
Tipp: tool for Taxonomic Identification and Phylogenetic Profiling
Tm-align: structural alignment of proteins
Tnseq-transit: statistical calculations of essentiality of genes or genomic regions
Toil: cross-platform workflow engine
Tombo: identification of modified nucleotides from raw nanopore sequencing data
Tophat: fast splice junction mapper for RNA-Seq reads
Tophat-recondition: post-processor for TopHat unmapped reads
Topp: set of programs implementing The OpenMS Proteomic Pipeline
Toppred: transmembrane topology prediction
Tortoize: Application to calculate ramachandran z-scores
Trace2dbest: bulk submission of chromatogram data to dbEST
Tracetuner: interpretation of DNA Sanger sequencing data
Transdecoder: find coding regions within RNA transcript sequences
Transrate-tools: helper for transrate
Transtermhp: find rho-independent transcription terminators in bacterial genomes
Tree-ppuzzle: Parallelized reconstruction of phylogenetic trees by maximum likelihood
Tree-puzzle: Reconstruction of phylogenetic trees by maximum likelihood
Treeview: Java re-implementation of Michael Eisen's TreeView
Treeviewx: Displays and prints phylogenetic trees
Trf: locate and display tandem repeats in DNA sequences
Trim-galore: automate quality and adapter trimming for DNA sequencing
Trimmomatic: flexible read trimming tool for Illumina NGS data
Trinityrnaseq: RNA-Seq De novo Assembly
Tvc: genetic variant caller for Ion Torrent sequencing platforms
Twopaco: build the compacted de Bruijn graph from many complete genomes
Uc-echo: error correction algorithm designed for short-reads from NGS
Ugene: integrated bioinformatics toolkit
Umap-learn: Uniform Manifold Approximation and Projection
Umis: tools for processing UMI RNA-tag data
Uncalled: Utility for Nanopore Current Alignment to Large Expanses of DNA
Unicycler: hybrid assembly pipeline for bacterial genomes
Unikmer: Toolkit for nucleic acid k-mer analysis
Varna: Visualization Applet for RNA
Vcfanno: annotate a VCF with other VCFs/BEDs/tabixed files
Vcftools: Collection of tools to work with VCF files
Velvet: Nucleic acid sequence assembler for very short reads
Velvet-long: Nucleic acid sequence assembler for very short reads, long version
Velvetoptimiser: automatically optimise Velvet do novo assembly parameters
Veryfasttree: Speeding up the estimation of phylogenetic trees from sequences
Vg: tools for working with genome variation graphs
Viewmol: graphical front end for computational chemistry programs
Virulencefinder: identify virulence genes in total or partial sequenced isolates of bacteria
Vmatch: large scale sequence analysis software
Vsearch: tool for processing metagenomic sequences
Vt: toolset for short variant discovery in genetic sequence data
Wham-align: Wisconsin's High-Throughput Alignment Method
Wigeon: reimplementation of the Pintail 16S DNA anomaly detection utility
Wise: comparison of biopolymers, like DNA and protein sequences
Xpore: Nanopore analysis of differential RNA modifications
Yaha: find split-read mappings on single-end queries
Yanagiba: filter low quality Oxford Nanopore reads basecalled with Albacore
Yanosim: read simulator nanopore DRS datasets

Official Debian packages with lower relevance

Adun.app: Molecular Simulator for GNUstep (GUI)
Catfishq: concatenates fastq files
Conda-package-handling: create and extract conda packages of various formats
Dascrubber: alignment-based scrubbing pipeline for DNA sequencing reads
Dnapi: adapter prediction for small RNA sequencing - utils
Emboss-explorer: web-based GUI to EMBOSS
Epigrass: scientific tool for simulations and scenario analysis in network epidemiology
Getdata: management of external databases
Hts-nim-tools: tools biological sequences: bam-filter, count-reads, vcf-check
Idseq-bench: Benchmark generator for the IDseq Portal
Illustrate: cartoonish representations of large biological molecules
Libhdf5-dev: HDF5 - development files - serial version
Libhnswlib-dev: fast approximate nearest neighbor search
Maude: high-performance logical framework
Metastudent-data: predictor of Gene Ontology terms from protein sequence - data files
Metastudent-data-2: predictor of Gene Ontology terms from protein sequence - data #2
Mrs: Information Retrieval System for Biomedical databanks
Python3-alignlib: edit and Hamming distances for biological sequences
Python3-anndata: annotated gene by sample numpy matrix
Python3-cgecore: Python3 module for the Center for Genomic Epidemiology
Python3-cyvcf2: VCF parser based on htslib (Python 3)
Python3-deeptools: platform for exploring biological deep-sequencing data
Python3-deeptoolsintervals: handlig GTF-like sequence-associated interal-annotation
Python3-htseq: Python3 high-throughput genome sequencing read analysis utilities
Python3-intake: lightweight package for finding and investigating data
Python3-loompy: access loom formatted files for bioinformatics
Python3-nanoget: extract information from Oxford Nanopore sequencing data and alignments
Python3-nanomath: simple math function for other Oxford Nanopore processing scripts
Python3-ncls: datastructure for interval overlap queries
Python3-py2bit: access to 2bit files
Python3-pybel: Biological Expression Language
Python3-pychopper: identify, orient and trim full-length Nanopore cDNA reads
Python3-pyfaidx: efficient random access to fasta subsequences for Python 3
Python3-pyflow: lightweight parallel task engine for Python
Python3-pyranges: 2D representation of genomic intervals and their annotations
Python3-pyrle: run length arithmetic in Python
Python3-pysam: interface for the SAM/BAM sequence alignment and mapping format (Python 3)
Python3-tinyalign: numerical representation of differences between strings
Q2-alignment: QIIME 2 plugin for generating and manipulating alignments
Q2-cutadapt: QIIME 2 plugin to work with adapters in sequence data
Q2-dada2: QIIME 2 plugin to work with adapters in sequence data
Q2-demux: QIIME 2 plugin for demultiplexing of sequence reads
Q2-emperor: QIIME2 plugin for display of ordination plots
Q2-feature-classifier: QIIME 2 plugin supporting taxonomic classification
Q2-feature-table: QIIME 2 plugin supporting operations on feature tables
Q2-fragment-insertion: QIIME 2 plugin for fragment insertion
Q2-metadata: QIIME 2 plugin for working with and visualizing Metadata
Q2-phylogeny: QIIME 2 plugin for phylogeny
Q2-quality-control: QIIME 2 plugin for quality assurance of feature and sequence data
Q2-quality-filter: QIIME2 plugin for PHRED-based filtering and trimming
Q2-sample-classifier: QIIME 2 plugin for machine learning prediction of sample data
Q2-taxa: QIIME 2 plugin for working with feature taxonomy annotations
Q2-types: QIIME 2 plugin defining types for microbiome analysis
Q2cli: Click-based command line interface for QIIME 2
Q2templates: Design template package for QIIME 2 Plugins
R-bioc-annotationhub: GNU R client to access AnnotationHub resources
R-bioc-aroma.light: BioConductor methods normalization and visualization of microarray data
R-bioc-beachmat: I/O for several formats storing matrix data
R-bioc-biocneighbors: Nearest Neighbor Detection for Bioconductor Packages
R-bioc-biocsingular: Singular Value Decomposition for Bioconductor Packages
R-bioc-ctc: Cluster and Tree Conversion
R-bioc-dnacopy: R package: DNA copy number data analysis
R-bioc-ensembldb: GNU R utilities to create and use an Ensembl based annotation database
R-bioc-experimenthub: BioConductor client to access ExperimentHub resources
R-bioc-geneplotter: R package of functions for plotting genomic data
R-bioc-genomicalignments: BioConductor representation and manipulation of short genomic alignments
R-bioc-genomicfiles: Distributed computing by file or by range
R-bioc-genomicranges: BioConductor representation and manipulation of genomic intervals
R-bioc-go.db: annotation maps describing the entire Gene Ontology
R-bioc-grohmm: GRO-seq Analysis Pipeline
R-bioc-gviz: Plotting data and annotation information along genomic coordinates
R-bioc-isoformswitchanalyzer: Identify, Annotate and Visualize Alternative Splicing and
R-bioc-org.hs.eg.db: genome-wide annotation for Human
R-bioc-qusage: qusage: Quantitative Set Analysis for Gene Expression
R-bioc-savr: GNU R parse and analyze Illumina SAV files
R-bioc-singlecellexperiment: S4 Classes for Single Cell Data
R-bioc-structuralvariantannotation: Variant annotations for structural variants
R-bioc-tximport: transcript-level estimates for biological sequencing
R-cran-amap: Another Multidimensional Analysis Package
R-cran-biwt: biweight mean vector and covariance and correlation
R-cran-boolnet: assembling, analyzing and visualizing Boolean networks
R-cran-corrplot: Visualization of a Correlation Matrix
R-cran-dynamictreecut: Methods for Detection of Clusters in Hierarchical Clustering
R-cran-epir: GNU R Functions for analysing epidemiological data
R-cran-fitdistrplus: support fit of parametric distribution
R-cran-forecast: GNU R forecasting functions for time series and linear models
R-cran-gprofiler2: Interface to the 'g:Profiler' Toolset
R-cran-minerva: Maximal Information-Based Nonparametric Exploration
R-cran-optimalcutpoints: Computing Optimal Cutpoints in Diagnostic Tests
R-cran-parmigene: Parallel Mutual Information to establish Gene Networks
R-cran-pheatmap: GNU R package to create pretty heatmaps
R-cran-qqman: R package for visualizing GWAS results using Q-Q and manhattan plots
R-cran-rcpphnsw: R bindings for a Library for Approximate Nearest Neighbors
R-cran-rentrez: GNU R interface to the NCBI's EUtils API
R-cran-sctransform: Variance Stabilizing Transformations for Single Cell UMI Data
Resfinder-db: ResFinder database is a curated database of acquired resistance genes
Science-workflow: workflow management systems useful for scientific research

Debian packages in contrib or non-free

Arb: phylogenetic sequence analysis suite - main program
Bcbio: toolkit for analysing high-throughput sequencing data
Blimps-utils: blocks database improved searcher
Caftools: maintenance of DNA sequence assemblies
Cluster3: Reimplementation of the Eisen-clustering software
Cufflinks: Transcript assembly, differential expression and regulation for RNA-Seq
Embassy-phylip: EMBOSS conversions of the programs in the phylip package
Raccoon: preparation of in silico drug screening projects
Relion-cuda: parallel toolkit for 3D reconstructions in cryo-electron microscopy
Relion-gui-cuda: toolkit for 3D reconstructions in cryo-electron microscopy (gui apps)
Seq-gen: simulate the evolution of nucleotide or amino acid sequences
Seqcluster: analysis of small RNA in NGS data
Sift: predicts if a substitution in a protein has a phenotypic effect
Solvate: arranges water molecules around protein structures
Trnascan-se: detection of transfer RNA genes in genomic sequence
Varscan: variant detection in next-generation sequencing data
Vdjtools: framework for post-analysis of B/T cell repertoires
Vienna-rna: RNA sequence analysis

Debian packages in New queue (hopefully available soon)

Coot: model building program for macromolecular crystallography

Packaging has started and developers might try the packaging code in VCS

Acacia: Error-corrector for pyrosequenced amplicon reads.
Agat: another GFF analysis toolkit
Amos-assembler: modular whole genome assembler
Apollo: genome annotation viewer and editor
Arvados: managing and analyzing biomedical big data
Axparafit: optimized statistical analysis of host-parasite coevolution
Axpcoords: highly optimized and parallelized porting of pcoords
Bagpipe: genomewide LD mapping
Bax2bam: Convert legacy PacBio Bax.H5, Bas.H5, and Ccs.H5 files to the new PacBio BAM format
Biceps: error-tolerant peptide identification
Bigsdb: Bacterial Isolate Genome Sequence Database
Bismark: bisulfite read mapper and methylation caller
Blat: BLAST-Like Alignment Tool
Blobology: tool set for the visualisation of genome assemblies
Braker: annotating protein coding genes in genomes.
Card-rgi: analysis of genome sequences using the Resistance Gene Identifier
Cellprofiler: quantitatively measure phenotypes from images automatically
Cinema: multi-sequence alignment editor and viewer
Condetri: straight-forward trimming of FASTQ sequences
Contrafold: CONditional TRAining for RNA Secondary Structure Prediction
Covpipe: pipeline to generate consensus sequences from NGS reads
Crossbow: Genotyping from short reads using cloud computing
Crux-toolkit: toolkit for tandem mass spectrometry analysis
Cytoscape: visualizing molecular interaction networks
Dazzle: Java-based DAS server
Deepbinner: demultiplexing barcoded Oxford Nanopore sequencing reads
Dendroscope: analyzing and visualizing rooted phylogenetic trees and networks
Diann: data-independent acquisition (DIA) proteomics data processing
Ecell: Concept and environment for constructing virtual cells on computers
Ensembl: basic Ensembl genome browser
Ensembl-vep: Variant Effect Predictor predicting the functional effects of genomic variants
Euler-sr: correcting errors in short gene sequence reads and assembling them
Euler2: de novo repeat classification and fragment assembly
Exabayes: bayesian phylogenetic tree inference for large-scale analyses
Ffp: Feature Frequency Profile Phylogeny
Fieldbioinformatics: pipeline with virus identification with Nanopore sequencer
Flappie: flip-flop basecaller for Oxford Nanopore reads
Forester: Graphical vizualiation tool Archaeopteryx
Galaxy: scientific workflow and data integration platform for computational biology
Gatk: The Genome Analysis Toolkit
Gerp++: identifies constrained elements in multiple alignments
Gramalign: multiple alignment of biological sequences
Graphbin: refined binning of metagenomic contigs using assembly graphs
Graphmap2: highly sensitive and accurate mapper for long, error-prone reads
Haploview: Analysis and visualization of LD and haplotype maps
Hawkeye: Interactive Visual Analytics Tool for Genome Assemblies
Htqc: Quality control and filtration for illumina sequencing data
Idefix: index checking for improved demultiplexing of NGS data
Inspect: mass-spectrometry database search tool
Jbrowse: genome browser with an AJAX-based interface
Kempbasu: significance tests for comparing digital gene expression profiles
Mach-haplotyper: Markov Chain based SNP haplotyper
Mage2tab: MAGE-MLv1 converter and visualiser
Manta: structural variant and indel caller for mapped sequencing data
Marginphase: simultaneous haplotyping and genotyping
Martj: distributed data integration system for biological data
Medaka: sequence correction provided by ONT Research
Meme: search for common motifs in DNA or protein sequences
Mesquite: modular system for evolutionary analysis
Metabit: analysing microbial profiles from high-throughput sequencing shotgun data
Modeller: Protein structure modeling by satisfaction of spatial restraints
Molekel: Advanced Interactive 3D-Graphics for Molecular Sciences
Mosaik-aligner: reference-guided aligner for next-generation sequencing
Mpsqed: alignment editor and multiplex pyrosequencing assay designer
Mugsy: multiple whole genome alignment tool
Mview: biological sequence alignment conversion
Nano-snakemake: detection of structural variants in genome sequencing data
Nanocall: Basecaller for Oxford Nanopore Sequencing Data
Nanocomp: compare multiple runs of long biological sequences
Nanoplot: plotting scripts for long read sequencing data
Ncbi-magicblast: RNA-seq mapping tool
Nextsv: automated structural variation detection for long-read sequencing
Ngila: global pairwise alignments with logarithmic and affine gap costs
Ngsqctoolkit: toolkit for the quality control of next generation sequencing data
Nw-align: global protein sequence alignment
Oases: de novo transcriptome assembler for very short reads
Omegamap: describing selection and recombination in sequences
Oncofuse: predicting oncogenic potential of gene fusions
Optitype: precision HLA typing from next-generation sequencing data
Paipline: Pipeline for the Automatic Identification of Pathogens
Pangolin: Phylogenetic Assignment of Named Global Outbreak LINeages
Partitionfinder: choses partitioning schemes and models of molecular evolution for sequence data
Patristic: Calculate patristic distances and comparing the components of genetic change
Pcma: fast and accurate multiple sequence alignment based on profile consistency
Phylophlan: microbial Tree of Life using 400 universal proteins
Phyloviz-core: phylogenetic inference and data visualization for sequence based typing methods
Pigx-scrnaseq: pipeline for checkpointed and distributed scRNA-seq analyses
Pipasic: Protein Abundance Correction in Metaproteomic Data
Plato: Analysis, translation, and organization of large-scale genetic data
Pomoxis: analysis components from Oxford Nanopore Research
Profit: Protein structure alignment
Psipred: protein secondary structure prediction
Pssh2: set of scripts for mapping protein sequence to structure
Pufferfish: Efficient index for the colored, compacted, de Bruijn graph
Purple: Picking Unique Relevant Peptides for viraL Experiments
Q2-composition: QIIME2 plugin for Compositional statistics
Q2-deblur: QIIME2 plugin to wrap the Deblur software for sequence quality control
Q2-diversity: QIIME2 plugin for core diversity analysis
Q2-gneiss: QIIME2 plugin for Compositional Data Analysis and Visualization
Q2-longitudinal: QIIME2 plugin for longitudinal studies and paired comparisons
Q2-vsearch: QIIME 2 plugin for clustering and dereplicating with vsearch
Qtlreaper: QTL analysis for expression data
Qualimap: evaluating next generation sequencing alignment data
Quast: Quality Assessment Tool for Genome Assemblies
R-bioc-mofa2: Multi-Omics Factor Analysis v2
R-bioc-org.mm.eg.db: genome wide annotation for Mouse
R-cran-drinsight: drug repurposing on transcriptome sequencing data
R-other-apmswapp: GNU R Pre- and Postprocessing For Affinity Purification Mass Spectrometry
R-other-fastbaps: A fast genetic clustering algorithm that approximates a Dirichlet Process Mixture model
Raxml-ng: phylogenetic tree inference tool which uses maximum-likelihood
Repeatmasker: screen DNA sequences for interspersed repeats
Roadtrips: case-control association testing with unknown population and pedigree structure
Rosa: Removal of Spurious Antisense in biological RNA sequences
Rsat: Regulatory Sequence Analysis Tools
Sailfish: RNA-seq expression estimation
Sap: Pairwise protein structure alignment via double dynamic programming
Seq-seq-pan: workflow for the SEQuential alignment of SEQuences
Seqwish: alignment to variation graph inducer
Signalalign: HMM-HDP models for MinION signal alignments
Sina: reference based multiple sequence alignment
Sistr: Salmonella In Silico Typing Resource (SISTR)
Situs: Modeling of atomic resolution structures into low-resolution density maps
Sourmash: tools for comparing DNA sequences with MinHash sketches
Sparta: automated reference-based bacterial RNA-seq Transcriptome Analysis
Ssaha: Sequence Search and Alignment by Hashing Algorithm
Strap: Comfortable and intuitive protein alignment editor / viewer
Strap-base: essential files for the interactive alignment viewer and editor Strap
Strelka: strelka2 germline and somatic small variant caller
Tab2mage: submitting large microarray experiment datasets to public repository database
Tacg: command line program for finding patterns in nucleic acids
Tandem-genotypes: compare lengths of duplications in DNA sequences
Tide: SEQUEST Searching for Peptide Identification from Tandem Mass Spectra
Tigr-glimmer-mg: finding genes in environmental shotgun DNA sequences
Tn-seqexplorer: explore and analyze Tn-seq data for prokaryotic genomes
Ufasta: utility to manipulate fasta files
Umap: quantify genome and methylome mappability
Unc-fish: Fast Identification of Segmental Homology
Varmatch: robust matching of small genomic variant datasets
Vmd: presentation of traces of molecular dynamics runs
Zodiac-zeden: ZODIAC - Zeden's Organise DIsplay And Compute

Unofficial packages built by somebody else

Big-blast: Helper tool to run blast on large sequences
Estferret: processes, clusters and annotates EST data
Maxd: data warehouse and visualisation environment for genomic expression data
Migrate: estimation of population sizes and gene flow using the coalescent
Msatfinder: identification and characterization of microsatellites in a comparative genomic context
Oligoarrayaux: Prediction of Melting Profiles for Nucleic Acids
Partigene: generating partial gemomes
Pfaat: Protein Family Alignment Annotation Tool
Prot4est: EST protein translation suite
Python3-orange: Data mining framework
Qtlcart: map quantitative traits using a map of molecular markers
Rbs-finder: find ribosome binding sites(RBS)
Roche454ace2caf: convert GS20 or FLX assemblies into CAF format
Splitstree: Analyzing and Visualizing Evolutionary Data
Taverna: designing and executing myGrid workflows for bioinformatics
Taxinspector: browser for entries in the NCBI taxonomy
Tetra: tetranucleotide frequency calculator

No known packages available but some record of interest (WNPP bug)

Btk-core: biomolecule Toolkit C++ library
Mirbase: The microRNA sequence database
Phylowin: Graphical interface for molecular phylogenetic inference

No known packages available

Amoscmp: comparative genome assembly package
Annovar: annotate genetic variants detected from diverse genomes
Arachne: toolkit for Whole Genome Shotgun Assembly
Asap: organize the data associated with a genome
Bambus: hierarchical approach to building contig scaffolds
Cactus
Cdna-db: quality-control checking of finished cDNA clone sequences
Cmap: view comparisons of genetic and physical maps
Contralign: parameter learning framework for protein pairwise sequence alignment
Copycat: fast access to cophylogenetic analyses
E-hive: distributed processing system based on 'autonomous agents'
Exalt: phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
Excavator: gene expression data clustering
Figaro: novel vector trimming software
Forge: genome assembler for mixed read types
Gbrowse-syn: Generic Synteny Browser
Genemark: family of gene prediction programs
Genesplicer: computational method for splice site prediction
Genetrack: genomic data storage and visualization framework
Genezilla: eukaryotic gene finder
Genographer: read data and reconstruct them into a gel image
Glimmerhmm: Eukaryotic Gene-Finding System
Gmv: comparative genome browser for Murasaki
Jigsaw: gene prediction using multiple sources of evidence
Maker2: annotate genomes and create genome databases
Metarep: JCVI Metagenomics Reports
Minimus: AMOS lightweight assembler
Mummergpu: High-throughput sequence alignment using Graphics Processing Units
Obo-edit: editor for biological ontologies
Operondb: detect and analyze conserved gene pairs
Phagefinder: heuristic computer program to identify prophage regions within bacterial genomes
Phpphylotree: draw phylogenetic trees
Phylographer: Graph Visualization Tool
Pyrophosphate-tools: for assembling and searching pyrophosphate sequence data
Rose: Region-Of-Synteny Extractor
Treebuilder3d: viewer of SAGE and other types of gene expression data
Tripal: collection of Drupal modules for genomic research
Twain: syntenic genefinder employing a Generalized Pair Hidden Markov Model
Uniprime: workflow-based platform for universal primer design
X-tandem-pipeline: peptide/protein identification from MS/MS mass spectra

Biology development - Debian Med packages for development of bioinformatics applications

This metapackage will install Debian packages which might be helpful for development of applications for biological research.

Official Debian packages with high relevance

Bio-tradis: analyse the output from TraDIS analyses of genomic sequences
Biobambam2: tools for early stage alignment file processing
Bioperl: Perl tools for computational molecular biology
Bioperl-run: BioPerl wrappers: scripts
Biosquid: utilities for biological sequence analysis
Cwltool: Common Workflow Language reference implementation
Gffread: GFF/GTF format conversions, region filtering, FASTA sequence extraction
Goby-java: next-generation sequencing data and results analysis tool
Libace-perl: Object-Oriented Access to ACEDB Databases
Libai-fann-perl: Perl wrapper for the FANN library
Libbambamc-dev: Development files for reading and writing BAM (genome alignment) files
Libbamtools-dev: C++ API for manipulating BAM (genome alignment) files
Libbigwig-dev: C library for handling bigWig files - header files
Libbio-alignio-stockholm-perl: stockholm sequence input/output stream
Libbio-asn1-entrezgene-perl: parser for NCBI Entrez Gene and NCBI Sequence records
Libbio-chado-schema-perl: DBIx::Class layer for the Chado database schema
Libbio-cluster-perl: BioPerl cluster modules
Libbio-coordinate-perl: BioPerl modules for working with biological coordinates
Libbio-das-lite-perl: implementation of the BioDas protocol
Libbio-db-biofetch-perl: Database object interface to BioFetch retrieval
Libbio-db-embl-perl: Database object interface for EMBL entry retrieval
Libbio-db-hts-perl: Perl interface to the HTS library
Libbio-db-ncbihelper-perl: collection of routines useful for queries to NCBI databases
Libbio-db-seqfeature-perl: Normalized feature for use with Bio::DB::SeqFeature::Store
Libbio-eutilities-perl: BioPerl interface to the Entrez Programming Utilities (E-utilities)
Libbio-featureio-perl: Modules for reading, writing, and manipulating sequence features
Libbio-graphics-perl: Generate GD images of Bio::Seq objects
Libbio-mage-perl: Container module for classes in the MAGE package: MAGE
Libbio-mage-utils-perl: Extra modules for classes in the MAGE package: MAGE
Libbio-primerdesigner-perl: Perl module to design PCR primers using primer3 and epcr
Libbio-samtools-perl: Perl interface to SamTools library for DNA sequencing
Libbio-scf-perl: Perl extension for reading and writing SCF sequence files
Libbio-tools-phylo-paml-perl: Bioperl interface to the PAML suite
Libbio-tools-run-alignment-clustalw-perl: Bioperl interface to Clustal W
Libbio-tools-run-alignment-tcoffee-perl: Bioperl interface to T-Coffee
Libbio-tools-run-remoteblast-perl: Object for remote execution of the NCBI Blast via HTTP
Libbio-variation-perl: BioPerl variation-related functionality
Libbiojava-java: Java API to biological data and applications (default version)
Libbiojava6-java: Java API to biological data and applications (version 6)
Libbioparser-dev: library for parsing several formats in bioinformatics
Libblasr-dev: tools for aligning PacBio reads to target sequences (development files)
Libbpp-core-dev: Bio++ Core library development files
Libbpp-phyl-dev: Bio++ Phylogenetic library development files
Libbpp-phyl-omics-dev: Bio++ Phylogenetics library: genomics components (development files)
Libbpp-popgen-dev: Bio++ Population Genetics library development files
Libbpp-qt-dev: Bio++ Qt Graphic classes library development files
Libbpp-raa-dev: Bio++ Remote Acnuc Access library development files
Libbpp-seq-dev: Bio++ Sequence library development files
Libbpp-seq-omics-dev: Bio++ Sequence library: genomics components (development files)
Libcdk-java: Chemistry Development Kit (CDK) Java libraries
Libchado-perl: database schema and tools for genomic data
Libcifpp-dev: Development files for libcifpp
Libconsensuscore-dev: algorithms for PacBio multiple sequence consensus -- development files
Libdivsufsort-dev: libdivsufsort header files
Libedlib-dev: library for sequence alignment using edit distance (devel)
Libfast5-dev: library for reading Oxford Nanopore Fast5 files -- headers
Libfastahack-dev: library for indexing and sequence extraction from FASTA files (devel)
Libffindex0-dev: library for simple index/database for huge amounts of small files (development)
Libfml-dev: development headers for libfml
Libgatbcore-dev: development library of the Genome Analysis Toolbox
Libgclib-dev: header files for Genome Code Lib (GCLib)
Libgenome-dev: toolkit for developing bioinformatic related software (devel)
Libgenome-model-tools-music-perl: module for finding mutations of significance in cancer
Libgenome-perl: pipelines, tools, and data management for genomics
Libgenometools0-dev: development files for GenomeTools
Libgff-dev: GFF/GTF parsing from cufflinks as a library
Libgkarrays-dev: library to query large collection of NGS sequences (development)
Libgo-perl: perl modules for GO and other OBO ontologies
Libhdf5-dev: HDF5 - development files - serial version
Libhmsbeagle-dev: High-performance lib for Bayesian and Maximum Likelihood phylogenetics (devel)
Libhts-dev: development files for the HTSlib
Libhtscodecs-dev: Development headers for custom compression for CRAM and others
Libhtsjdk-java: Java API for high-throughput sequencing data (HTS) formats
Libjebl2-java: Java Evolutionary Biology Library
Libjloda-java: Java library of data structures and algorithms for bioinformatics
Libkmer-dev: suite of tools for DNA sequence analysis (development lib)
Libmems-dev: development library to support DNA string matching and comparative genomics
Libminimap2-dev: development headers for libminimap
Libmmblib-dev: development files of MacroMoleculeBuilder
Libmuscle-dev: multiple alignment development library for protein sequences
Libncbi-vdb-dev: libraries for using data in the INSDC Sequence Read Archives (devel)
Libncbi6-dev: NCBI libraries for biology applications (development files)
Libncl-dev: NEXUS Class Library (static lib and header files)
Libngs-java: Next Generation Sequencing language Bindings (Java bindings)
Libngs-sdk-dev: Next Generation Sequencing language Bindings (development)
Libnhgri-blastall-perl: Perl extension for running and parsing NCBI's BLAST 2.x
Libopenmm-dev: C++ header files for the OpenMM library
Libopenms-dev: library for LC/MS data management and analysis - dev files
Libpal-java: Phylogenetic Analysis Library
Libparasail-dev: Development heaaders and static libraries for parasail
Libpbbam-dev: Pacific Biosciences binary alignment/map (BAM) library (headers)
Libpbdata-dev: tools for handling PacBio sequences (development files)
Libpbihdf-dev: tools for handling PacBio hdf5 files (development files)
Libpbseq-dev: library for analyzing PacBio sequencing data (development files)
Libpdb-redo-dev: Development files for libpdb-redo
Libpll-dev: Phylogenetic Likelihood Library (development)
Libpwiz-dev: library to perform proteomics data analyses (devel files)
Libqes-dev: DNA sequence parsing library -- development
Librcsb-core-wrapper0-dev: development files for librcsb-core-wrapper0t64
Librdp-taxonomy-tree-java: taxonomy tree library from Ribosomal Database Project (RDP)
Librelion-dev: C++ API for RELION (3D reconstructions in cryo-electron microscopy)
Librg-blast-parser-perl: very fast NCBI BLAST parser - binding for Perl
Librg-reprof-bundle-perl: protein secondary structure and accessibility predictor (perl module)
Librostlab-blast0-dev: very fast C++ library for parsing the output of NCBI BLAST programs (devel)
Librostlab3-dev: C++ library for computational biology (development)
Libsbml5-dev: System Biology Markup Language library - development files
Libseqan2-dev: C++ library for the analysis of biological sequences (development)
Libseqan3-dev: C++ library for the analysis of biological sequences v3 (development)
Libseqlib-dev: C++ htslib/bwa-mem/fermi interface for interrogating sequence data (dev)
Libslow5-dev: header and static library for reading & writing SLOW5 files
Libsmithwaterman-dev: determine similar regions between two strings or genomic sequences (devel)
Libsnp-sites1-dev: Static libraries and header files for the package snp-sites
Libsort-key-top-perl: Perl module to select and sort top n elements of a list
Libspoa-dev: SIMD partial order alignment library (development files)
Libsrf-dev: C++ implementation of the SRF format for DNA sequence data
Libssm-dev: macromolecular superposition library - development files
Libssu-dev: high-performance phylogenetic diversity calculations (dev)
Libssw-dev: Development headers and static libraries for libssw
Libssw-java: Java bindings for libssw
Libstaden-read-dev: development files for libstaden-read
Libstatgen-dev: development files for the libStatGen
Libswiss-perl: Perl API to the UniProt database
Libtabixpp-dev: C++ wrapper to tabix indexer (development files)
Libthread-pool-dev: C++ header-only thread pool library (devel)
Libvcflib-dev: C++ library for parsing and manipulating VCF files (development)
Libvibrant6-dev: NCBI libraries for graphic biology applications (development files)
Libwfa2-dev: exact gap-affine algorithm (development)
Libzerg-perl: fast perl module for parsing the output of NCBI BLAST programs
Libzerg0-dev: development libraries and header files for libzerg
Mcl: Markov Cluster algorithm
Nim-hts-dev: wrapper for hts C library
Nim-kexpr-dev: kexpr math expressions for nim
Nim-lapper-dev: simple, fast interval searches for nim
Ont-fast5-api: simple interface to HDF5 files of the Oxford Nanopore .fast5 file format
Pyfai: Fast Azimuthal Integration scripts
Python3-airr: Data Representation Standard library for antibody and TCR sequences
Python3-anndata: annotated gene by sample numpy matrix
Python3-bcbio-gff: Python3 library to read and write Generic Feature Format
Python3-bioframe: library to enable flexible, scalable operations on genomic interval dataframes
Python3-biom-format: Biological Observation Matrix (BIOM) format (Python 3)
Python3-biomaj3: BioMAJ workflow management library
Python3-biopython: Python3 library for bioinformatics
Python3-biotools: Python3 bioinformatics utilities for high-throughput genomic sequencing
Python3-bx: library to manage genomic data and its alignment
Python3-cgecore: Python3 module for the Center for Genomic Epidemiology
Python3-cigar: manipulate SAM cigar strings
Python3-cobra: constraint-based modeling of biological networks with Python 3
Python3-cogent3: framework for genomic biology
Python3-cooler: library for a sparse, compressed, binary persistent storage
Python3-corepywrap: library that exports C++ mmCIF accessors to Python3
Python3-csb: Python framework for structural bioinformatics (Python3 version)
Python3-cutadapt: Clean biological sequences from high-throughput sequencing reads (Python 3)
Python3-cyvcf2: VCF parser based on htslib (Python 3)
Python3-deeptools: platform for exploring biological deep-sequencing data
Python3-deeptoolsintervals: handlig GTF-like sequence-associated interal-annotation
Python3-dendropy: DendroPy Phylogenetic Computing Library (Python 3)
Python3-dnaio: Python 3 library for fast parsing of FASTQ and FASTA files
Python3-ete3: Python Environment for (phylogenetic) Tree Exploration - Python 3.X
Python3-fast5: library for reading Oxford Nanopore Fast5 files -- Python 3
Python3-freecontact: fast protein contact predictor - binding for Python3
Python3-gfapy: flexible and extensible software library for handling sequence graphs
Python3-gffutils: Work with GFF and GTF files in a flexible database framework
Python3-gtfparse: parser for gene transfer format (aka GFF2)
Python3-htseq: Python3 high-throughput genome sequencing read analysis utilities
Python3-intervaltree-bio: Interval tree convenience classes for genomic data -- Python 3 library
Python3-kineticstools: detection of DNA modifications (Python 3 library)
Python3-loompy: access loom formatted files for bioinformatics
Python3-mirtop: annotate miRNAs with a standard mirna/isomir naming (Python 3)
Python3-nanoget: extract information from Oxford Nanopore sequencing data and alignments
Python3-ngs: Next Generation Sequencing language Bindings (Python3 bindings)
Python3-pairix: 1D/2D indexing and querying with a pair of genomic coordinates
Python3-pangolearn: store of the trained model for pangolin to access
Python3-parasail: Python3 bindings for the parasail C library
Python3-pbcommand: common command-line interface for Pacific Biosciences analysis modules
Python3-pbconsensuscore: algorithms for PacBio multiple sequence consensus -- Python 3
Python3-pbcore: Python 3 library for processing PacBio data files
Python3-peptidebuilder: generate atomic oligopeptide 3D structure from sequence
Python3-presto: toolkit for processing B and T cell sequences (Python3 module)
Python3-propka: heuristic pKa calculations with ligands (Python 3)
Python3-py2bit: access to 2bit files
Python3-pyabpoa: adaptive banded Partial Order Alignment - python3 module
Python3-pyani: Python3 module for average nucleotide identity analyses
Python3-pybedtools: Python 3 wrapper around BEDTools for bioinformatics work
Python3-pybel: Biological Expression Language
Python3-pybigwig: Python 3 module for quick access to bigBed and bigWig files
Python3-pyfaidx: efficient random access to fasta subsequences for Python 3
Python3-pyfastx: fast random access to sequences from FASTA/Q file - python3 module
Python3-pymummer: Python 3 interface to MUMmer
Python3-pyranges: 2D representation of genomic intervals and their annotations
Python3-pysam: interface for the SAM/BAM sequence alignment and mapping format (Python 3)
Python3-pyspoa: Python bindings to spoa
Python3-pyvcf: Variant Call Format (VCF) parser for Python 3
Python3-rdkit: Collection of cheminformatics and machine-learning software
Python3-ruffus: Python3 computation pipeline library widely used in bioinformatics
Python3-screed: short nucleotide read sequence utils in Python 3
Python3-shasta: nanopore whole genome assembly (dynamic library)
Python3-skbio: Python3 data structures, algorithms, educational resources for bioinformatic
Python3-slow5: Python3 modul for reading & writing SLOW5 files
Python3-sqt: SeQuencing Tools for biological DNA/RNA high-throughput data
Python3-streamz: build pipelines to manage continuous streams of data
Python3-tinyalign: numerical representation of differences between strings
Python3-torch: Tensors and Dynamic neural networks in Python (Python Interface)
Python3-treetime: inference of time stamped phylogenies and ancestral reconstruction (Python 3)
Python3-unifrac: high-performance phylogenetic diversity calculations
Python3-wdlparse: Workflow Description Language (WDL) parser for Python
R-bioc-biobase: base functions for Bioconductor
R-cran-boolnet: assembling, analyzing and visualizing Boolean networks
R-cran-corrplot: Visualization of a Correlation Matrix
R-cran-distory: GNU R distance between phylogenetic histories
R-cran-fitdistrplus: support fit of parametric distribution
R-cran-forecast: GNU R forecasting functions for time series and linear models
R-cran-genetics: GNU R package for population genetics
R-cran-gprofiler2: Interface to the 'g:Profiler' Toolset
R-cran-haplo.stats: GNU R package for haplotype analysis
R-cran-metamix: GNU R bayesian mixture analysis for metagenomic community profiling
R-cran-phangorn: GNU R package for phylogenetic analysis
R-cran-pheatmap: GNU R package to create pretty heatmaps
R-cran-phylobase: GNU R base package for phylogenetic structures and comparative data
R-cran-pscbs: R package: Analysis of Parent-Specific DNA Copy Numbers
R-cran-qqman: R package for visualizing GWAS results using Q-Q and manhattan plots
R-cran-rentrez: GNU R interface to the NCBI's EUtils API
R-cran-rncl: GNU R interface to the Nexus Class Library
R-cran-rnexml: GNU R package for semantically rich I/O for the 'NeXML' format
R-cran-rotl: GNU R interface to the 'Open Tree of Life' API
R-cran-samr: GNU R significance analysis of microarrays
R-cran-sctransform: Variance Stabilizing Transformations for Single Cell UMI Data
R-cran-seqinr: GNU R biological sequences retrieval and analysis
R-cran-seurat: Tools for Single Cell Genomics
R-cran-tsne: t-distributed stochastic neighbor embedding for R (t-SNE)
R-cran-vegan: Community Ecology Package for R
R-cran-webgestaltr: find over-represented properties in gene lists
Ruby-bio: Ruby tools for computational molecular biology
Ruby-crb-blast: Run conditional reciprocal best blast
Sbmltoolbox: libsbml toolbox for octave and matlab
Snakemake: pythonic workflow management system
Toil: cross-platform workflow engine

Official Debian packages with lower relevance

Capsule-nextflow: packaging and deployment tool for Java applications
Conda-package-handling: create and extract conda packages of various formats
Ctdconverter: Convert CTD files into Galaxy tool and CWL CommandLineTool files
Cthreadpool-dev: minimal ANSI C thread pool - development files
Cwlformat: code formatter for Common Workflow Language
Cwltest: Common Workflow Language testing framework
Libargs-dev: simple header-only C++ argument parser library
Libbam-dev: manipulates nucleotide sequence alignments in BAM or SAM format
Libbbhash-dev: bloom-filter based minimal perfect hash function library
Libbifrost-dev: static library and header files for libbifrost
Libbiojava4-java: Java API to biological data and applications (default version)
Libbiosoup-dev: C++ header-only support library for bioinformatics tools
Libbtllib-dev: Bioinformatics Technology Lab common code library
Libcapsule-maven-nextflow-java: packaging tool for Java applications with Maven coordinates
Libconcurrentqueue-dev: industrial-strength lock-free queue for C++
Libdisorder-dev: library for entropy measurement of byte streams (devel)
Libfreecontact-dev: fast protein contact predictor library - development files
Libfreecontact-doc: documentation for libfreecontact
Libfreecontact-perl: fast protein contact predictor - binding for Perl
Libgatk-bwamem-java: interface to call Heng Li's bwa mem aligner from Java code
Libgatk-bwamem-jni: interface to call Heng Li's bwa mem aligner from Java code (jni)
Libgatk-fermilite-java: interface to call Heng Li's fermi-lite assembler from Java code
Libgatk-fermilite-jni: interface to call Heng Li's fermi-lite assembler from Java code (jni)
Libgatk-native-bindings-java: library of native bindings for gatk and picard-tools
Libgenomicsdb-dev: sparse array storage library for genomics (development files)
Libgenomicsdb-java: sparse array storage library for genomics (Java library)
Libicb-utils-java: Java library of utilities to manage files and compute statistics
Libmaus2-dev: collection of data structures and algorithms for biobambam (devel)
Libmilib-java: library for Next Generation Sequencing (NGS) data processing
Libminimap-dev: development headers for libminimap
Libmodhmm-dev: library for constructing, training and scoring hidden Markov models (dev)
Libpbcopper-dev: data structures, algorithms, and utilities for C++ applications -- header files
Librostlab-blast-doc: very fast C++ library for parsing the output of NCBI BLAST programs (doc)
Librostlab-doc: C++ library for computational biology (documentation)
Libsavvy-dev: C++ interface for the SAV file format
Libsuma-dev: headers and static library for sumatra and sumaclust
Libsvmloc-dev: PSORTb adapted library for svm machine-learning library (dev)
Libterraces-dev: enumerate terraces in phylogenetic tree space (development lib)
Libtfbs-perl: scanning DNA sequence with a position weight matrix
Libvbz-hdf-plugin-dev: VBZ compression plugin for nanopore signal data (devel)
Libxxsds-dynamic-dev: succinct and compressed fully-dynamic data structures library
Python-biopython-doc: Documentation for the Biopython library
Python3-alignlib: edit and Hamming distances for biological sequences
Python3-bel-resources: Python3 utilities for BEL resource files
Python3-bioblend: CloudMan and Galaxy API library (Python 3)
Python3-biopython-sql: Biopython support for the BioSQL database schema (Python 3)
Python3-cgelib: Python3 code to be utilized across the CGE tools
Python3-conda-package-streaming: fetch conda metadata
Python3-ctdopts: Gives your Python tools a CTD-compatible interface
Python3-intake: lightweight package for finding and investigating data
Python3-joypy: ridgeline-/joyplots plotting routine
Python3-ncls: datastructure for interval overlap queries
Python3-networkx: tool to create, manipulate and study complex networks (Python3)
Python3-pycosat: Python bindings to picosat
Python3-pyflow: lightweight parallel task engine for Python
Q2-alignment: QIIME 2 plugin for generating and manipulating alignments
Q2-cutadapt: QIIME 2 plugin to work with adapters in sequence data
Q2-dada2: QIIME 2 plugin to work with adapters in sequence data
Q2-demux: QIIME 2 plugin for demultiplexing of sequence reads
Q2-emperor: QIIME2 plugin for display of ordination plots
Q2-feature-classifier: QIIME 2 plugin supporting taxonomic classification
Q2-feature-table: QIIME 2 plugin supporting operations on feature tables
Q2-fragment-insertion: QIIME 2 plugin for fragment insertion
Q2-metadata: QIIME 2 plugin for working with and visualizing Metadata
Q2-phylogeny: QIIME 2 plugin for phylogeny
Q2-quality-control: QIIME 2 plugin for quality assurance of feature and sequence data
Q2-quality-filter: QIIME2 plugin for PHRED-based filtering and trimming
Q2-sample-classifier: QIIME 2 plugin for machine learning prediction of sample data
Q2-taxa: QIIME 2 plugin for working with feature taxonomy annotations
Q2-types: QIIME 2 plugin defining types for microbiome analysis
Q2cli: Click-based command line interface for QIIME 2
Q2templates: Design template package for QIIME 2 Plugins
Qiime: Quantitative Insights Into Microbial Ecology
R-bioc-affxparser: Affymetrix File Parsing SDK
R-bioc-affy: BioConductor methods for Affymetrix Oligonucleotide Arrays
R-bioc-affyio: BioConductor tools for parsing Affymetrix data files
R-bioc-altcdfenvs: BioConductor alternative CDF environments
R-bioc-annotate: BioConductor annotation for microarrays
R-bioc-annotationdbi: GNU R Annotation Database Interface for BioConductor
R-bioc-annotationhub: GNU R client to access AnnotationHub resources
R-bioc-aroma.light: BioConductor methods normalization and visualization of microarray data
R-bioc-arrayexpress: access to the ArrayExpress Microarray Database at EBI
R-bioc-biocgenerics: generic functions for Bioconductor
R-bioc-biocneighbors: Nearest Neighbor Detection for Bioconductor Packages
R-bioc-biomart: GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)
R-bioc-biomformat: GNU R interface package for the BIOM file format
R-bioc-biostrings: GNU R string objects representing biological sequences
R-bioc-biovizbase: GNU R basic graphic utilities for visualization of genomic data
R-bioc-bitseq: transcript expression inference and analysis for RNA-seq data
R-bioc-bsgenome: BioConductor infrastructure for Biostrings-based genome data packages
R-bioc-cner: CNE Detection and Visualization
R-bioc-complexheatmap: make complex heatmaps using GNU R
R-bioc-ctc: Cluster and Tree Conversion
R-bioc-cummerbund: tool for analysis of Cufflinks RNA-Seq output
R-bioc-dada2: sample inference from amplicon sequencing data
R-bioc-deseq2: R package for RNA-Seq Differential Expression Analysis
R-bioc-dnacopy: R package: DNA copy number data analysis
R-bioc-ebseq: R package for RNA-Seq Differential Expression Analysis
R-bioc-ensembldb: GNU R utilities to create and use an Ensembl based annotation database
R-bioc-genefilter: methods for filtering genes from microarray experiments
R-bioc-geneplotter: R package of functions for plotting genomic data
R-bioc-genomeinfodb: BioConductor utilities for manipulating chromosome identifiers
R-bioc-genomicalignments: BioConductor representation and manipulation of short genomic alignments
R-bioc-genomicfeatures: GNU R tools for making and manipulating transcript centric annotations
R-bioc-genomicranges: BioConductor representation and manipulation of genomic intervals
R-bioc-geoquery: Get data from NCBI Gene Expression Omnibus (GEO)
R-bioc-go.db: annotation maps describing the entire Gene Ontology
R-bioc-graph: handle graph data structures for BioConductor
R-bioc-gseabase: Gene set enrichment data structures and methods
R-bioc-gsva: Gene Set Variation Analysis for microarray and RNA-seq data
R-bioc-gviz: Plotting data and annotation information along genomic coordinates
R-bioc-hypergraph: BioConductor hypergraph data structures
R-bioc-impute: Imputation for microarray data
R-bioc-iranges: GNU R low-level containers for storing sets of integer ranges
R-bioc-limma: linear models for microarray data
R-bioc-makecdfenv: BioConductor CDF Environment Maker
R-bioc-mergeomics: Integrative network analysis of omics data
R-bioc-metagenomeseq: GNU R statistical analysis for sparse high-throughput sequencing
R-bioc-mofa: Multi-Omics Factor Analysis (MOFA)
R-bioc-multiassayexperiment: Software for integrating multi-omics experiments in BioConductor
R-bioc-nanostringqcpro: ??? missing short description for package r-bioc-nanostringqcpro :-(
R-bioc-oligo: Preprocessing tools for oligonucleotide arrays
R-bioc-oligoclasses: Classes for high-throughput arrays supported by oligo and crlmm
R-bioc-org.hs.eg.db: genome-wide annotation for Human
R-bioc-pcamethods: BioConductor collection of PCA methods
R-bioc-phyloseq: GNU R handling and analysis of high-throughput microbiome census data
R-bioc-preprocesscore: BioConductor collection of pre-processing functions
R-bioc-purecn: copy number calling and SNV classification using targeted short read sequencing
R-bioc-qusage: qusage: Quantitative Set Analysis for Gene Expression
R-bioc-rbgl: R interface to the graph algorithms contained in the BOOST library
R-bioc-rsamtools: GNU R binary alignment (BAM), variant call (BCF), or tabix file import
R-bioc-rtracklayer: GNU R interface to genome browsers and their annotation tracks
R-bioc-s4vectors: BioConductor S4 implementation of vectors and lists
R-bioc-savr: GNU R parse and analyze Illumina SAV files
R-bioc-shortread: GNU R classes and methods for high-throughput short-read sequencing data
R-bioc-snpstats: BioConductor SnpMatrix and XSnpMatrix classes and methods
R-bioc-structuralvariantannotation: Variant annotations for structural variants
R-bioc-tfbstools: GNU R Transcription Factor Binding Site (TFBS) Analysis
R-bioc-titancna: Subclonal copy number and LOH prediction from whole genome sequencing
R-bioc-tximport: transcript-level estimates for biological sequencing
R-bioc-variantannotation: BioConductor annotation of genetic variants
R-bioc-xvector: BioConductor representation and manpulation of external sequences
R-cran-adegenet: GNU R exploratory analysis of genetic and genomic data
R-cran-adephylo: GNU R exploratory analyses for the phylogenetic comparative method
R-cran-amap: Another Multidimensional Analysis Package
R-cran-biwt: biweight mean vector and covariance and correlation
R-cran-dt: GNU R wrapper of the JavaScript library 'DataTables'
R-cran-dynamictreecut: Methods for Detection of Clusters in Hierarchical Clustering
R-cran-fastcluster: Fast hierarchical clustering routines for GNU R
R-cran-future.apply: apply function to elements in parallel using futures
R-cran-future.batchtools: Future API for Parallel and Distributed Processing
R-cran-ica: Independent Component Analysis
R-cran-itertools: Iterator Tools
R-cran-kaos: Encoding of Sequences Based on Frequency Matrix Chaos
R-cran-metap: Meta-Analysis of Significance Values
R-cran-minerva: Maximal Information-Based Nonparametric Exploration
R-cran-natserv: GNU R 'NatureServe' Interface
R-cran-nmf: GNU R framework to perform non-negative matrix factorization
R-cran-optimalcutpoints: Computing Optimal Cutpoints in Diagnostic Tests
R-cran-parmigene: Parallel Mutual Information to establish Gene Networks
R-cran-pcapp: Robust PCA by Projection Pursuit
R-cran-proc: Display and Analyze ROC Curves
R-cran-rann: Fast Nearest Neighbour Search Using L2 Metric
R-cran-rcpphnsw: R bindings for a Library for Approximate Nearest Neighbors
R-cran-robustrankaggreg: Methods for robust rank aggregation
R-cran-rocr: GNU R package to prepare and display ROC curves
R-cran-rook: web server interface for R
R-cran-rsvd: Randomized Singular Value Decomposition
R-cran-shazam: Immunoglobulin Somatic Hypermutation Analysis
R-cran-sitmo: GNU R parallel pseudo random number generator 'sitmo' header files
R-cran-venndiagram: Generate High-Resolution Venn and Euler Plots
Ruby-rgfa: parse, edit and write GFA format graphs in Ruby

Debian packages in contrib or non-free

Python3-bcbio: library for analysing high-throughput sequencing data
Python3-seqcluster: analysis of small RNA in NGS data
Vdjtools: framework for post-analysis of B/T cell repertoires

Packaging has started and developers might try the packaging code in VCS

Libatomicqueue-dev: devel files for C++ atomic_queue library
Libfast-perl: FAST Analysis of Sequences Toolbox
Libforester-java: Libraries for evolutionary biology and comparative genomics research
Libnexml-java: Java API for NeXML
Python3-compclust: explore and quantify relationships between clustering results
Python3-consensuscore2: generate consensus sequences for PacBio data -- Python 3
Python3-galaxy-lib: Subset of Galaxy core code base designed to be used
Python3-misopy: Mixture of Isoforms model for RNA-Seq isoform quantitation (Python 3)
Python3-scanpy: Single-Cell Analysis in Python
Q2-composition: QIIME2 plugin for Compositional statistics
Q2-deblur: QIIME2 plugin to wrap the Deblur software for sequence quality control
Q2-diversity: QIIME2 plugin for core diversity analysis
Q2-gneiss: QIIME2 plugin for Compositional Data Analysis and Visualization
Q2-longitudinal: QIIME2 plugin for longitudinal studies and paired comparisons
Q2-vsearch: QIIME 2 plugin for clustering and dereplicating with vsearch
R-bioc-bridgedbr: identifier mapping between biological databases
R-cran-drinsight: drug repurposing on transcriptome sequencing data
R-other-apmswapp: GNU R Pre- and Postprocessing For Affinity Purification Mass Spectrometry

No known packages available

Bioclipse: platform for chemo- and bioinformatics based on Eclipse
Octace-bioinfo: Bioinformatics manipulation for Octave

Next generation sequencing - Debian Med bioinformatics applications usable in Next Generation Sequencing

It aims at gettting packages which specialize in the processing or interpretation of data generated with next- (and later-) generation high-thoughput sequencing technologies.

Official Debian packages with high relevance

Anfo: Short Read Aligner/Mapper from MPG
Arden: specificity control for read alignments using an artificial reference
Art-nextgen-simulation-tools: simulation tools to generate synthetic next-generation sequencing reads
Artfastqgenerator: outputs artificial FASTQ files derived from a reference genome
Bamtools: toolkit for manipulating BAM (genome alignment) files
Bcftools: genomic variant calling and manipulation of VCF/BCF files
Bedtools: suite of utilities for comparing genomic features
Berkeley-express: Streaming quantification for high-throughput sequencing
Bio-rainbow: clustering and assembling short reads for bioinformatics
Blasr: mapping single-molecule sequencing reads
Bowtie: Ultrafast memory-efficient short read aligner
Bowtie2: ultrafast memory-efficient short read aligner
Bwa: Burrows-Wheeler Aligner
Canu: single molecule sequence assembler for genomes
Changeo: Repertoire clonal assignment toolkit (Python 3)
Crac: integrated RNA-Seq read analysis
Cutadapt: Clean biological sequences from high-throughput sequencing reads
Daligner: local alignment discovery between long nucleotide sequencing reads
Deepnano: alternative basecaller for MinION reads of genomic sequences
Discosnp: discovering Single Nucleotide Polymorphism from raw set(s) of reads
Dnaclust: tool for clustering millions of short DNA sequences
Dwgsim: short sequencing read simulator
Ea-utils: command-line tools for processing biological sequencing data
Fastaq: FASTA and FASTQ file manipulation tools
Fastp: Ultra-fast all-in-one FASTQ preprocessor
Fastqc: quality control for high throughput sequence data
Flexbar: flexible barcode and adapter removal for sequencing platforms
Fml-asm: tool for assembling Illumina short reads in small regions
Fsm-lite: frequency-based string mining (lite)
Giira: RNA-Seq driven gene finding incorporating ambiguous reads
Grinder: Versatile omics shotgun and amplicon sequencing read simulator
Hilive: realtime alignment of Illumina reads
Hinge: long read genome assembler based on hinging
Hisat2: graph-based alignment of short nucleotide reads to many genomes
Idba: iterative De Bruijn Graph short read assemblers
Igdiscover: analyzes antibody repertoires to find new V genes
Igor: infers V(D)J recombination processes from sequencing data
Igv: Integrative Genomics Viewer
Iva: iterative virus sequence assembler
Khmer: in-memory DNA sequence kmer counting, filtering & graph traversal
Kissplice: Detection of various kinds of polymorphisms in RNA-seq data
Kraken: assigning taxonomic labels to short DNA sequences
Kraken2: taxonomic classification system using exact k-mer matches
Last-align: genome-scale comparison of biological sequences
Libvcflib-tools: C++ library for parsing and manipulating VCF files (tools)
Macs: Model-based Analysis of ChIP-Seq on short reads sequencers
Mapdamage: tracking and quantifying damage patterns in ancient DNA sequences
Mapsembler2: bioinformatics targeted assembly software
Maq: maps short fixed-length polymorphic DNA sequence reads to reference sequences
Maqview: graphical read alignment viewer for short gene sequences
Mhap: locality-sensitive hashing to detect long-read overlaps
Microbiomeutil: Microbiome Analysis Utilities
Mira-assembler: Whole Genome Shotgun and EST Sequence Assembler
Mothur: sequence analysis suite for research on microbiota
Nanopolish: consensus caller for nanopore sequencing data
Paleomix: pipelines and tools for the processing of ancient and modern HTS data
Pbhoney: genomic structural variation discovery
Pbjelly: genome assembly upgrading tool
Pbsuite: software for Pacific Biosciences sequencing data
Picard-tools: Command line tools to manipulate SAM and BAM files
Pirs: Profile based Illumina pair-end Reads Simulator
Pizzly: Identifies gene fusions in RNA sequencing data
Placnet: Plasmid Constellation Network project
Poretools: toolkit for nanopore nucleotide sequencing data
Python3-airr: Data Representation Standard library for antibody and TCR sequences
Python3-gffutils: Work with GFF and GTF files in a flexible database framework
Python3-presto: toolkit for processing B and T cell sequences (Python3 module)
Python3-pybedtools: Python 3 wrapper around BEDTools for bioinformatics work
Python3-sqt: SeQuencing Tools for biological DNA/RNA high-throughput data
Q2cli: Click-based command line interface for QIIME 2
Qcumber: quality control of genomic sequences
Qiime: Quantitative Insights Into Microbial Ecology
Quorum: QUality Optimized Reads of genomic sequences
R-bioc-deseq2: R package for RNA-Seq Differential Expression Analysis
R-bioc-edger: Empirical analysis of digital gene expression data in R
R-bioc-hilbertvis: GNU R package to visualise long vector data
R-bioc-metagenomeseq: GNU R statistical analysis for sparse high-throughput sequencing
R-bioc-rsubread: Subread Sequence Alignment and Counting for R
R-cran-alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis
R-cran-shazam: Immunoglobulin Somatic Hypermutation Analysis
R-cran-tcr: Advanced Data Analysis of Immune Receptor Repertoires
R-cran-tigger: Infers new Immunoglobulin alleles from Rep-Seq Data
Rna-star: ultrafast universal RNA-seq aligner
Rtax: Classification of sequence reads of 16S ribosomal RNA gene
Salmon: wicked-fast transcript quantification from RNA-seq data
Sambamba: tools for working with SAM/BAM data
Samblaster: marks duplicates, extracts discordant/split reads
Samtools: processing sequence alignments in SAM, BAM and CRAM formats
Scoary: pangenome-wide association studies
Scythe: Bayesian adaptor trimmer for sequencing reads
Seqprep: stripping adaptors and/or merging paired reads of DNA sequences with overlap
Seqtk: Fast and lightweight tool for processing sequences in the FASTA or FASTQ format
Sga: de novo genome assembler that uses string graphs
Sickle: windowed adaptive trimming tool for FASTQ files using quality
Smalt: Sequence Mapping and Alignment Tool
Smrtanalysis: software suite for single molecule, real-time sequencing
Snap-aligner: Scalable Nucleotide Alignment Program
Sniffles: structural variation caller using third-generation sequencing
Snp-sites: Binary code for the package snp-sites
Snpomatic: fast, stringent short-read mapping software
Soapdenovo: short-read assembly method to build de novo draft assembly
Soapdenovo2: short-read assembly method to build de novo draft assembly
Sortmerna: tool for filtering, mapping and OTU-picking NGS reads
Spades: genome assembler for single-cell and isolates data sets
Sprai: single-pass sequencing read accuracy improver
Sra-toolkit: utilities for the NCBI Sequence Read Archive
Srst2: Short Read Sequence Typing for Bacterial Pathogens
Ssake: genomics application for assembling millions of very short DNA sequences
Stacks: pipeline for building loci from short-read DNA sequences
Stringtie: assemble short RNAseq reads to transcripts
Subread: toolkit for processing next-gen sequencing data
Sumaclust: fast and exact clustering of genomic sequences
Sumatra: fast and exact comparison and clustering of sequences
Tabix: generic indexer for TAB-delimited genome position files
Transrate-tools: helper for transrate
Trimmomatic: flexible read trimming tool for Illumina NGS data
Trinityrnaseq: RNA-Seq De novo Assembly
Uc-echo: error correction algorithm designed for short-reads from NGS
Vcftools: Collection of tools to work with VCF files
Velvet: Nucleic acid sequence assembler for very short reads
Velvet-long: Nucleic acid sequence assembler for very short reads, long version
Velvetoptimiser: automatically optimise Velvet do novo assembly parameters
Vsearch: tool for processing metagenomic sequences
Wham-align: Wisconsin's High-Throughput Alignment Method
Wigeon: reimplementation of the Pintail 16S DNA anomaly detection utility

Official Debian packages with lower relevance

Nanolyse: remove lambda phage reads from a fastq file
Python3-anndata: annotated gene by sample numpy matrix
R-bioc-isoformswitchanalyzer: Identify, Annotate and Visualize Alternative Splicing and

Debian packages in contrib or non-free

Bcbio: toolkit for analysing high-throughput sequencing data
Cufflinks: Transcript assembly, differential expression and regulation for RNA-Seq
Vdjtools: framework for post-analysis of B/T cell repertoires

Packaging has started and developers might try the packaging code in VCS

Graphmap2: highly sensitive and accurate mapper for long, error-prone reads
Mosaik-aligner: reference-guided aligner for next-generation sequencing
Nanoplot: plotting scripts for long read sequencing data
R-bioc-mofa2: Multi-Omics Factor Analysis v2
Umap: quantify genome and methylome mappability

No known packages available

Annovar: annotate genetic variants detected from diverse genomes
Forge: genome assembler for mixed read types

Phylogeny - Debian Med phylogeny packages

This lists Debian packages related to phylogeny for use in life sciences. The purpose of this compilation of packages is to have a handy subset of from the med-bio metapackage which contains a lot more than only phylogeny related software.

Official Debian packages with high relevance

Altree: program to perform phylogeny-based association and localization analysis
Beast-mcmc: Bayesian MCMC phylogenetic inference
Clustalw: global multiple nucleotide or peptide sequence alignment
Clustalx: Multiple alignment of nucleic acid and protein sequences (graphical interface)
Dialign: Segment-based multiple sequence alignment
Dialign-tx: Segment-based multiple sequence alignment
Exonerate: generic tool for pairwise sequence comparison
Fastdnaml: Tool for construction of phylogenetic trees of DNA sequences
Fasttree: phylogenetic trees from alignments of nucleotide or protein sequences
Figtree: graphical phylogenetic tree viewer
Gmap: spliced and SNP-tolerant alignment for mRNA and short reads
Hmmer: profile hidden Markov models for protein sequence analysis
Iqtree: efficient phylogenetic software by maximum likelihood
Jmodeltest: HPC selection of models of nucleotide substitution
Kalign: Global and progressive multiple sequence alignment
Mrbayes: Bayesian Inference of Phylogeny
Muscle: Multiple alignment program of protein sequences
Muscle3: multiple alignment program of protein sequences
Mustang: multiple structural alignment of proteins
Njplot: phylogenetic tree drawing program
Phylip: package of programs for inferring phylogenies
Phyml: Phylogenetic estimation using Maximum Likelihood
Poa: Partial Order Alignment for multiple sequence alignment
Populations: population genetic software
Pplacer: phylogenetic placement and downstream analysis
Proalign: Probabilistic multiple alignment program
Probalign: multiple sequence alignment using partition function posterior probabilities
Probcons: PROBabilistic CONSistency-based multiple sequence alignment
Proda: multiple alignment of protein sequences
Prottest: selection of best-fit models of protein evolution
Quicktree: Neighbor-Joining algorithm for phylogenies
Seaview: Multiplatform interface for sequence alignment and phylogeny
Sigma-align: Simple greedy multiple alignment of non-coding DNA sequences
Spread-phy: analyze and visualize phylogeographic reconstructions
T-coffee: Multiple Sequence Alignment
Tm-align: structural alignment of proteins
Tree-ppuzzle: Parallelized reconstruction of phylogenetic trees by maximum likelihood
Tree-puzzle: Reconstruction of phylogenetic trees by maximum likelihood
Treeview: Java re-implementation of Michael Eisen's TreeView
Treeviewx: Displays and prints phylogenetic trees
Veryfasttree: Speeding up the estimation of phylogenetic trees from sequences

Official Debian packages with lower relevance

Python3-treetime: inference of time stamped phylogenies and ancestral reconstruction (Python 3)

Packaging has started and developers might try the packaging code in VCS

Forester: Graphical vizualiation tool Archaeopteryx
Patristic: Calculate patristic distances and comparing the components of genetic change

No known packages available but some record of interest (WNPP bug)

Phylowin: Graphical interface for molecular phylogenetic inference

No known packages available

Gbioseq: DNA sequence editor for Linux
Jstreeview: Editor for Phylogenetic Trees
Phpphylotree: draw phylogenetic trees
Treetime: Bayesian sampling of phylogenetic trees from molecular data

Cloud - Debian Med bioinformatics applications usable in cloud computing

This metapackage will install Debian packages related to molecular biology, structural biology and bioinformatics for use in life sciences, that do not depend on graphical toolkits and therefore can fit on system images for use in cloud computing clusters, where space can be limited.

Official Debian packages with high relevance

Abyss: de novo, parallel, sequence assembler for short reads
Acedb-other: retrieval of DNA or protein sequences
Aevol: digital genetics model to run Evolution Experiments in silico
Alien-hunter: Interpolated Variable Order Motifs to identify horizontally acquired DNA
Altree: program to perform phylogeny-based association and localization analysis
Amap-align: Protein multiple alignment by sequence annealing
Ampliconnoise: removal of noise from 454 sequenced PCR amplicons
Anfo: Short Read Aligner/Mapper from MPG
Aragorn: tRNA and tmRNA detection in nucleotide sequences
Arden: specificity control for read alignments using an artificial reference
Autodock: analysis of ligand binding to protein structure
Autodock-vina: docking of small molecules to proteins
Autogrid: pre-calculate binding of ligands to their receptor
Bamtools: toolkit for manipulating BAM (genome alignment) files
Bedtools: suite of utilities for comparing genomic features
Bioperl: Perl tools for computational molecular biology
Bioperl-run: BioPerl wrappers: scripts
Biosquid: utilities for biological sequence analysis
Blast2: transitional dummy package to ncbi-blast+-legacy
Bowtie: Ultrafast memory-efficient short read aligner
Bowtie2: ultrafast memory-efficient short read aligner
Boxshade: Pretty-printing of multiple sequence alignments
Bwa: Burrows-Wheeler Aligner
Cassiopee: index and search tool in genomic sequences
Cd-hit: suite of programs designed to quickly group sequences
Cdbfasta: Constant DataBase indexing and retrieval tools for multi-FASTA files
Circos: plotter for visualizing data
Clearcut: extremely efficient phylogenetic tree reconstruction
Clonalframe: inference of bacterial microevolution using multilocus sequence data
Clustalo: General-purpose multiple sequence alignment program for proteins
Clustalw: global multiple nucleotide or peptide sequence alignment
Concavity: predictor of protein ligand binding sites from structure and conservation
Conservation-code: protein sequence conservation scoring tool
Datamash: statistics tool for command-line interface
Dialign: Segment-based multiple sequence alignment
Dialign-tx: Segment-based multiple sequence alignment
Discosnp: discovering Single Nucleotide Polymorphism from raw set(s) of reads
Disulfinder: cysteines disulfide bonding state and connectivity predictor
Dnaclust: tool for clustering millions of short DNA sequences
Dssp: protein secondary structure assignment based on 3D structure
Embassy-domainatrix: Extra EMBOSS commands to handle domain classification file
Embassy-domalign: Extra EMBOSS commands for protein domain alignment
Embassy-domsearch: Extra EMBOSS commands to search for protein domains
Emboss: European molecular biology open software suite
Exonerate: generic tool for pairwise sequence comparison
Fastdnaml: Tool for construction of phylogenetic trees of DNA sequences
Fastlink: faster version of pedigree programs of Linkage
Fastqc: quality control for high throughput sequence data
Fasttree: phylogenetic trees from alignments of nucleotide or protein sequences
Fitgcp: fitting genome coverage distributions with mixture models
Flexbar: flexible barcode and adapter removal for sequencing platforms
Freecontact: fast protein contact predictor
Gasic: genome abundance similarity correction
Genometools: versatile genome analysis toolkit
Gff2aplot: pair-wise alignment-plots for genomic sequences in PostScript
Gff2ps: produces PostScript graphical output from GFF-files
Giira: RNA-Seq driven gene finding incorporating ambiguous reads
Glam2: gapped protein motifs from unaligned sequences
Gmap: spliced and SNP-tolerant alignment for mRNA and short reads
Grinder: Versatile omics shotgun and amplicon sequencing read simulator
Gromacs: Molecular dynamics simulator, with building and analysis tools
Hhsuite: sensitive protein sequence searching based on HMM-HMM alignment
Hisat2: graph-based alignment of short nucleotide reads to many genomes
Hmmer: profile hidden Markov models for protein sequence analysis
Idba: iterative De Bruijn Graph short read assemblers
Infernal: inference of RNA secondary structural alignments
Jellyfish: count k-mers in DNA sequences
Kalign: Global and progressive multiple sequence alignment
Kissplice: Detection of various kinds of polymorphisms in RNA-seq data
Last-align: genome-scale comparison of biological sequences
Loki: MCMC linkage analysis on general pedigrees
Macs: Model-based Analysis of ChIP-Seq on short reads sequencers
Mafft: Multiple alignment program for amino acid or nucleotide sequences
Mapsembler2: bioinformatics targeted assembly software
Maq: maps short fixed-length polymorphic DNA sequence reads to reference sequences
Melting: compute the melting temperature of nucleic acid duplex
Minia: short-read biological sequence assembler
Mipe: Tools to store PCR-derived data
Mira-assembler: Whole Genome Shotgun and EST Sequence Assembler
Mlv-smile: Find statistically significant patterns in sequences
Mothur: sequence analysis suite for research on microbiota
Mrbayes: Bayesian Inference of Phylogeny
Mummer: Efficient sequence alignment of full genomes
Muscle: Multiple alignment program of protein sequences
Muscle3: multiple alignment program of protein sequences
Mustang: multiple structural alignment of proteins
Ncbi-epcr: Tool to test a DNA sequence for the presence of sequence tagged sites
Ncbi-tools-bin: NCBI libraries for biology applications (text-based utilities)
Ncoils: coiled coil secondary structure prediction
Neobio: computes alignments of amino acid and nucleotide sequences
Paraclu: Parametric clustering of genomic and transcriptomic features
Parsinsert: Parsimonious Insertion of unclassified sequences into phylogenetic trees
Pdb2pqr: Preparation of protein structures for electrostatics calculations
Perm: efficient mapping of short reads with periodic spaced seeds
Phyml: Phylogenetic estimation using Maximum Likelihood
Phyutility: simple analyses or modifications on both phylogenetic trees and data matrices
Picard-tools: Command line tools to manipulate SAM and BAM files
Plink: whole-genome association analysis toolset
Plink1.9: whole-genome association analysis toolset
Plink2: whole-genome association analysis toolset
Poa: Partial Order Alignment for multiple sequence alignment
Prank: Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
Prime-phylo: bayesian estimation of gene trees taking the species tree into account
Primer3: tool to design flanking oligo nucleotides for DNA amplification
Probabel: Toolset for Genome-Wide Association Analysis
Probcons: PROBabilistic CONSistency-based multiple sequence alignment
Proda: multiple alignment of protein sequences
Prodigal: Microbial (bacterial and archaeal) gene finding program
Python3-biomaj3-cli: BioMAJ client
Python3-biopython: Python3 library for bioinformatics
Python3-cogent3: framework for genomic biology
Qiime: Quantitative Insights Into Microbial Ecology
R-bioc-edger: Empirical analysis of digital gene expression data in R
R-bioc-hilbertvis: GNU R package to visualise long vector data
R-cran-pvclust: Hierarchical Clustering with P-Values via Multiscale Bootstrap
R-cran-qtl: GNU R package for genetic marker linkage analysis
R-cran-vegan: Community Ecology Package for R
R-other-mott-happy.hbrem: GNU R package for fine-mapping complex diseases
Raster3d: tools for generating images of proteins or other molecules
Readseq: Conversion between sequence formats
Rnahybrid: Fast and effective prediction of microRNA/target duplexes
Rtax: Classification of sequence reads of 16S ribosomal RNA gene
Samtools: processing sequence alignments in SAM, BAM and CRAM formats
Seqan-apps: C++ library for the analysis of biological sequences
Sibsim4: align expressed RNA sequences on a DNA template
Sigma-align: Simple greedy multiple alignment of non-coding DNA sequences
Sim4: tool for aligning cDNA and genomic DNA
Smalt: Sequence Mapping and Alignment Tool
Snap: location of genes from DNA sequence with hidden markov model
Soapdenovo: short-read assembly method to build de novo draft assembly
Soapdenovo2: short-read assembly method to build de novo draft assembly
Squizz: Converter for genetic sequences and alignments
Sra-toolkit: utilities for the NCBI Sequence Read Archive
Ssake: genomics application for assembling millions of very short DNA sequences
Staden-io-lib-utils: programs for manipulating DNA sequencing files
T-coffee: Multiple Sequence Alignment
Tabix: generic indexer for TAB-delimited genome position files
Theseus: superimpose macromolecules using maximum likelihood
Tigr-glimmer: Gene detection in archea and bacteria
Tree-ppuzzle: Parallelized reconstruction of phylogenetic trees by maximum likelihood
Tree-puzzle: Reconstruction of phylogenetic trees by maximum likelihood
Vcftools: Collection of tools to work with VCF files
Velvet: Nucleic acid sequence assembler for very short reads
Veryfasttree: Speeding up the estimation of phylogenetic trees from sequences
Wise: comparison of biopolymers, like DNA and protein sequences

Debian packages in contrib or non-free

Cufflinks: Transcript assembly, differential expression and regulation for RNA-Seq
Embassy-phylip: EMBOSS conversions of the programs in the phylip package

Packaging has started and developers might try the packaging code in VCS

Bagpipe: genomewide LD mapping

Content management - Debian Med content management systems

Here you can find software that is useful to build a content management system for medical care.

Packaging has started and developers might try the packaging code in VCS

Xnat: platform for data management and productivity tasks in neuroimaging
Zope-zms: Content management for science, technology and medicine

No known packages available

Hid: database management system for clinical imaging

Covid-19 - This task exists only for tagging COVID-19 relevant cases

The Debian Med team intends to take part at the

 COVID-19 Biohackathon (April 5-11, 2020)
This task was created only for the purpose to list relevant packages.

Official Debian packages with high relevance

Abacas: close gaps in genomic alignments from short reads
Abyss: de novo, parallel, sequence assembler for short reads
Allelecount: NGS copy number algorithms
Assembly-stats: get assembly statistics from FASTA and FASTQ files
Augur: pipeline components for real-time virus analysis
Bamclipper: Remove gene-specific primer sequences from SAM/BAM alignments
Bamkit: tools for common BAM file manipulations
Bbmap: BBTools genomic aligner and other tools for short sequences
Bcalm: de Bruijn compaction in low memory
Bcftools: genomic variant calling and manipulation of VCF/BCF files
Bedtools: suite of utilities for comparing genomic features
Biobambam2: tools for early stage alignment file processing
Bowtie2: ultrafast memory-efficient short read aligner
Busco: benchmarking sets of universal single-copy orthologs
Bustools: program for manipulating BUS files for single cell RNA-Seq datasets
Bwa: Burrows-Wheeler Aligner
Cat-bat: taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Centrifuge: rapid and memory-efficient system for classification of DNA sequences
Changeo: Repertoire clonal assignment toolkit (Python 3)
Chip-seq: tools performing common ChIP-Seq data analysis tasks
Clonalframeml: Efficient Inference of Recombination in Whole Bacterial Genomes
Conquest-common: ConQuest DICOM Server - common files
Cutadapt: Clean biological sequences from high-throughput sequencing reads
Cwltool: Common Workflow Language reference implementation
Dcmtk: OFFIS DICOM toolkit command line utilities
Delly: Structural variant discovery by read analysis
Dextractor: (d)extractor and compression command library
Diamond-aligner: accelerated BLAST compatible local sequence aligner
Discosnp: discovering Single Nucleotide Polymorphism from raw set(s) of reads
Drop-seq-tools: analyzing Drop-seq data
Epigrass: scientific tool for simulations and scenario analysis in network epidemiology
Fasta3: tools for searching collections of biological sequences
Fastani: Fast alignment-free computation of whole-genome Average Nucleotide Identity
Fastp: Ultra-fast all-in-one FASTQ preprocessor
Fastqc: quality control for high throughput sequence data
Filtlong: quality filtering tool for long reads of genome sequences
Flash: Fast Length Adjustment of SHort reads
Flye: de novo assembler for single molecule sequencing reads using repeat graphs
Freebayes: Bayesian haplotype-based polymorphism discovery and genotyping
Genometools: versatile genome analysis toolkit
Gffread: GFF/GTF format conversions, region filtering, FASTA sequence extraction
Ginkgocadx: Medical Imaging Software and complete DICOM Viewer
Gnumed-client: medical practice management - Client
Gnumed-server: medical practice management - server
Gromacs: Molecular dynamics simulator, with building and analysis tools
Gubbins: phylogenetic analysis of genome sequences
Imagej: Image processing program with a focus on microscopy images
Ivar: functions broadly useful for viral amplicon-based sequencing
Kalign: Global and progressive multiple sequence alignment
Kallisto: near-optimal RNA-Seq quantification
Kraken2: taxonomic classification system using exact k-mer matches
Lastz: pairwise aligning DNA sequences
Libbbhash-dev: bloom-filter based minimal perfect hash function library
Libchipcard-dev: API for smartcard readers
Libgclib-dev: header files for Genome Code Lib (GCLib)
Libgdcm-tools: Grassroots DICOM tools and utilities
Libhtscodecs-dev: Development headers for custom compression for CRAM and others
Libics-dev: Image Cytometry Standard file reading and writing (devel)
Libmaus2-dev: collection of data structures and algorithms for biobambam (devel)
Libmilib-java: library for Next Generation Sequencing (NGS) data processing
Libseqan3-dev: C++ library for the analysis of biological sequences v3 (development)
Lighter: fast and memory-efficient sequencing error corrector
Lumpy-sv: general probabilistic framework for structural variant discovery
Mecat2: ultra-fast and accurate de novo assembly tools for SMRT reads
Megahit: ultra-fast and memory-efficient meta-genome assembler
Metabat: robust statistical framework for reconstructing genomes from metagenomic data
Minia: short-read biological sequence assembler
Minimap2: versatile pairwise aligner for genomic and spliced nucleotide sequences
Mmb: model the structure and dynamics of macromolecules
Mmseqs2: ultra fast and sensitive protein search and clustering
Multiqc: output integration for RNA sequencing across tools and samples
Muscle: Multiple alignment program of protein sequences
Muscle3: multiple alignment program of protein sequences
Nanofilt: filtering and trimming of long read sequencing data
Nanolyse: remove lambda phage reads from a fastq file
Nanook: pre- and post-alignment analysis of nanopore sequencing data
Nanopolish: consensus caller for nanopore sequencing data
Nanosv: structural variant caller for nanopore data
Ncbi-blast+: next generation suite of BLAST sequence search tools
Ngmlr: CoNvex Gap-cost alignMents for Long Reads
Nthash: Methods to evaluate runtime and uniformity tests for hashing methods
Odil: C++11 library for the DICOM standard (application)
Orthanc: Lightweight, RESTful DICOM server for medical imaging
Orthanc-dicomweb: Plugin to extend Orthanc with support of WADO and DICOMweb
Orthanc-python: Develop plugins for Orthanc using the Python programming language
Orthanc-wsi: Whole-slide imaging support for Orthanc (digital pathology)
Paleomix: pipelines and tools for the processing of ancient and modern HTS data
Parallel-fastq-dump: parallel fastq-dump wrapper
Parasail: Aligner based on libparasail
Picard-tools: Command line tools to manipulate SAM and BAM files
Picopore: lossless compression of Nanopore files
Pigx-rnaseq: pipeline for checkpointed and distributed RNA-seq analyses
Pinfish: Collection of tools to annotate genomes using long read transcriptomics data
Plasmidid: mapping-based, assembly-assisted plasmid identification tool
Plink1.9: whole-genome association analysis toolset
Plink2: whole-genome association analysis toolset
Plip: fully automated protein-ligand interaction profiler
Porechop: adapter trimmer for Oxford Nanopore reads
Poretools: toolkit for nanopore nucleotide sequencing data
Pplacer: phylogenetic placement and downstream analysis
Presto: toolkit for processing B and T cell sequences
Prinseq-lite: PReprocessing and INformation of SEQuence data (lite version)
Prokka: rapid annotation of prokaryotic genomes
Proteinortho: Detection of (Co-)orthologs in large-scale protein analysis
Pybedtools-bin: Scripts produced for pybedtools
Pycoqc: computes metrics and generates Interactive QC plots
Pyomo: PYthon Optimization Modeling Objects
Python3-biom-format: Biological Observation Matrix (BIOM) format (Python 3)
Python3-biopython: Python3 library for bioinformatics
Python3-bx: library to manage genomic data and its alignment
Python3-cgecore: Python3 module for the Center for Genomic Epidemiology
Python3-cogent3: framework for genomic biology
Python3-cooler: library for a sparse, compressed, binary persistent storage
Python3-cyvcf2: VCF parser based on htslib (Python 3)
Python3-depinfo: retrieve and print Python 3 package dependencies
Python3-drmaa: interface to DRMAA-compliant distributed resource management systems
Python3-etelemetry: lightweight Python3 client to communicate with the etelemetry server
Python3-gffutils: Work with GFF and GTF files in a flexible database framework
Python3-htseq: Python3 high-throughput genome sequencing read analysis utilities
Python3-nanoget: extract information from Oxford Nanopore sequencing data and alignments
Python3-nanomath: simple math function for other Oxford Nanopore processing scripts
Python3-pairix: 1D/2D indexing and querying with a pair of genomic coordinates
Python3-pairtools: Framework to process sequencing data from a Hi-C experiment
Python3-pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads
Python3-pbcommand: common command-line interface for Pacific Biosciences analysis modules
Python3-pbcore: Python 3 library for processing PacBio data files
Python3-pyani: Python3 module for average nucleotide identity analyses
Python3-pychopper: identify, orient and trim full-length Nanopore cDNA reads
Python3-pydicom: DICOM medical file reading and writing (Python 3)
Python3-pyfaidx: efficient random access to fasta subsequences for Python 3
Python3-pynn: simulator-independent specification of neuronal network models
Python3-pysam: interface for the SAM/BAM sequence alignment and mapping format (Python 3)
Python3-questplus: QUEST+ implementation in Python3
Python3-scitrack: Python3 library to track scientific data
Python3-screed: short nucleotide read sequence utils in Python 3
Python3-seirsplus: Models of SEIRS epidemic dynamics with extensions
Python3-streamz: build pipelines to manage continuous streams of data
Python3-tinyalign: numerical representation of differences between strings
Python3-toolz: List processing tools and functional utilities
Python3-torch: Tensors and Dynamic neural networks in Python (Python Interface)
Python3-tornado: scalable, non-blocking web server and tools - Python 3 package
Python3-treetime: inference of time stamped phylogenies and ancestral reconstruction (Python 3)
Python3-typed-ast: ??? missing short description for package python3-typed-ast :-(
Python3-vcf: Variant Call Format (VCF) parser for Python 3
Q2-cutadapt: QIIME 2 plugin to work with adapters in sequence data
Q2-feature-table: QIIME 2 plugin supporting operations on feature tables
Q2-quality-filter: QIIME2 plugin for PHRED-based filtering and trimming
Qcat: demultiplexing Oxford Nanopore reads from FASTQ files
Quicktree: Neighbor-Joining algorithm for phylogenies
R-bioc-htsfilter: GNU R filter replicated high-throughput transcriptome sequencing data
R-bioc-limma: linear models for microarray data
R-bioc-mutationalpatterns: GNU R comprehensive genome-wide analysis of mutational processes
R-bioc-pwmenrich: PWM enrichment analysis
R-bioc-rcpi: molecular informatics toolkit for compound-protein interaction
R-bioc-rgsepd: GNU R gene set enrichment / projection displays
R-bioc-rsamtools: GNU R binary alignment (BAM), variant call (BCF), or tabix file import
R-bioc-tcgabiolinks: GNU R/Bioconductor package for integrative analysis with GDC data
R-cran-alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis
R-cran-covid19us: cases of COVID-19 in the United States prepared for GNU R
R-cran-diagnosismed: medical diagnostic test accuracy analysis toolkit
R-cran-epi: GNU R epidemiological analysis
R-cran-epibasix: GNU R Elementary Epidemiological Functions
R-cran-epicalc: GNU R Epidemiological calculator
R-cran-epiestim: GNU R estimate time varying reproduction numbers from rpidemic curves
R-cran-epir: GNU R Functions for analysing epidemiological data
R-cran-epitools: GNU R Epidemiology Tools for Data and Graphics
R-cran-hms: GNU R pretty time of day
R-cran-incidence: GNU R compute, handle, plot and model incidence of dated events
R-cran-kernelheaping: GNU R kernel density estimation for heaped and rounded data
R-cran-lexrankr: extractive summarization of text with the LexRank algorithm
R-cran-mediana: clinical trial simulations
R-cran-msm: GNU R Multi-state Markov and hidden Markov models in continuous time
R-cran-qtl: GNU R package for genetic marker linkage analysis
R-cran-seroincidence: GNU R seroincidence calculator tool
R-cran-sf: Simple Features for R
R-cran-shazam: Immunoglobulin Somatic Hypermutation Analysis
R-cran-sjplot: GNU R data visualization for statistics in social science
R-cran-spp: GNU R ChIP-seq processing pipeline
R-cran-stringi: GNU R character string processing facilities
R-cran-surveillance: GNU R package for the Modeling and Monitoring of Epidemic Phenomena
R-cran-tigger: Infers new Immunoglobulin alleles from Rep-Seq Data
R-other-ascat: Allele-Specific Copy Number Analysis of Tumours
Ragout: Reference-Assisted Genome Ordering UTility
Readucks: Nanopore read de-multiplexer (read demux -> readux -> readucks, innit)
Recan: genetic distance plotting for recombination events analysis
Rna-star: ultrafast universal RNA-seq aligner
Rsem: RNA-Seq by Expectation-Maximization
Ruby-bio: Ruby tools for computational molecular biology
Salmon: wicked-fast transcript quantification from RNA-seq data
Samblaster: marks duplicates, extracts discordant/split reads
Samclip: filter SAM file for soft and hard clipped alignments
Samtools: processing sequence alignments in SAM, BAM and CRAM formats
Scrappie: basecaller for Nanopore sequencer
Sepp: phylogeny with ensembles of Hidden Markov Models
Seqkit: cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Seqmagick: imagemagick-like frontend to Biopython SeqIO
Shapeit4: fast and accurate method for estimation of haplotypes (phasing)
Shiny-server: put Shiny web apps online
Shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
Smrtanalysis: software suite for single molecule, real-time sequencing
Snakemake: pythonic workflow management system
Snpeff: genetic variant annotation and effect prediction toolbox - tool
Snpsift: tool to annotate and manipulate genome variants - tool
Spades: genome assembler for single-cell and isolates data sets
Spaln: splicing-aware transcript-alignment to genomic DNA
Staden-io-lib-utils: programs for manipulating DNA sequencing files
Stringtie: assemble short RNAseq reads to transcripts
Sumaclust: fast and exact clustering of genomic sequences
Texlive-science: TeX Live: Mathematics, natural sciences, computer science packages
Thesias: Testing Haplotype Effects In Association Studies
Tiddit: structural variant calling
Tipp: tool for Taxonomic Identification and Phylogenetic Profiling
Tnseq-transit: statistical calculations of essentiality of genes or genomic regions
Toil: cross-platform workflow engine
Tombo: identification of modified nucleotides from raw nanopore sequencing data
Tophat-recondition: post-processor for TopHat unmapped reads
Trinculo: toolkit to carry out genetic association for multi-category phenotypes
Umap-learn: Uniform Manifold Approximation and Projection
Umis: tools for processing UMI RNA-tag data
Uncalled: Utility for Nanopore Current Alignment to Large Expanses of DNA
Unicycler: hybrid assembly pipeline for bacterial genomes
Vg: tools for working with genome variation graphs
Vsearch: tool for processing metagenomic sequences
Vt: toolset for short variant discovery in genetic sequence data
Workrave: Repetitive Strain Injury prevention tool
Wtdbg2: de novo sequence assembler for long noisy reads
Yanagiba: filter low quality Oxford Nanopore reads basecalled with Albacore
Yanosim: read simulator nanopore DRS datasets

Official Debian packages with lower relevance

Libsimde-dev: Implementations of SIMD instructions for all systems
Python3-anndata: annotated gene by sample numpy matrix
Python3-mmtf: binary encoding of biological structures (Python 3)
R-bioc-rsubread: Subread Sequence Alignment and Counting for R

Debian packages in contrib or non-free

Bcbio: toolkit for analysing high-throughput sequencing data
Python3-seqcluster: analysis of small RNA in NGS data
Varscan: variant detection in next-generation sequencing data
Vienna-rna: RNA sequence analysis

Debian packages in experimental

Libtensorflow-framework2: Computation using data flow graphs for scalable machine learning

Packaging has started and developers might try the packaging code in VCS

Arvados: managing and analyzing biomedical big data
Auspice: web app for visualizing pathogen evolution
Blat: BLAST-Like Alignment Tool
Chime: COVID-19 Hospital Impact Model for Epidemics
Covpipe: pipeline to generate consensus sequences from NGS reads
Ensembl-vep: Variant Effect Predictor predicting the functional effects of genomic variants
Fieldbioinformatics: pipeline with virus identification with Nanopore sequencer
Flappie: flip-flop basecaller for Oxford Nanopore reads
Graphmap2: highly sensitive and accurate mapper for long, error-prone reads
Manta: structural variant and indel caller for mapped sequencing data
Medaka: sequence correction provided by ONT Research
Nanoplot: plotting scripts for long read sequencing data
Ncbi-magicblast: RNA-seq mapping tool
Nextflow: DSL for data-driven computational pipelines
Nextstrain-ncov: Nextstrain build for novel coronavirus (nCoV)
Nf-core-artic: nf-core ARTIC field bioinformatics viral genome pipeline
Oncofuse: predicting oncogenic potential of gene fusions
Optitype: precision HLA typing from next-generation sequencing data
Pangolin: Phylogenetic Assignment of Named Global Outbreak LINeages
Pomoxis: analysis components from Oxford Nanopore Research
Python3-idseq-dag: Pipeline engine for IDseq (Python 3)
Python3-scanpy: Single-Cell Analysis in Python
Qualimap: evaluating next generation sequencing alignment data
Quast: Quality Assessment Tool for Genome Assemblies
R-cran-covid19: GNU R Coronavirus COVID-19 data acquisition and visualization
R-other-fastbaps: A fast genetic clustering algorithm that approximates a Dirichlet Process Mixture model
Rosa: Removal of Spurious Antisense in biological RNA sequences
Sailfish: RNA-seq expression estimation
Seqwish: alignment to variation graph inducer
Signalalign: HMM-HDP models for MinION signal alignments
Streamlit: fast way to build custom ML tools
Strelka: strelka2 germline and somatic small variant caller
Ufasta: utility to manipulate fasta files
Vadr: classification and annotation of viral sequences

Medical data - Debian Med drug databases

This metapackage will install free drug databases and related applications. The database can be accessed by any EMR using the application.

Official Debian packages with high relevance

Freediams: pharmaceutical drug prescription and interaction manager
Freemedforms-freedata: free extra-data for the FreeMedForms project
Python3-hl7: Python3 library for parsing HL7 messages

Official Debian packages with lower relevance

Oscar: Open Source CPAP Analysis Reporter (OSCAR)

No known packages available

Drugref.org: pharmaceutical reference database

Dental - Debian Med packages related to dental practice

This metapackage contains dependencies for a collection of software which might be helpful for dentists to manage their practice.

Official Debian packages with high relevance

Entangle: Tethered Camera Control & Capture
Imagetooth: library generating images of teeth for odontograms
Openmolar: dental practice management software

Epidemiology - Debian Med epidemiology related packages

This metapackage will install tools that are useful in epidemiological research. Several packages making use of the GNU R data language for statistical investigation. It might be a good idea to read the paper "A short introduction to R for Epidemiology" at http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf

Official Debian packages with high relevance

Epigrass: scientific tool for simulations and scenario analysis in network epidemiology
Python3-seirsplus: Models of SEIRS epidemic dynamics with extensions
Python3-torch: Tensors and Dynamic neural networks in Python (Python Interface)
Python3-treetime: inference of time stamped phylogenies and ancestral reconstruction (Python 3)
R-cran-covid19us: cases of COVID-19 in the United States prepared for GNU R
R-cran-diagnosismed: medical diagnostic test accuracy analysis toolkit
R-cran-epi: GNU R epidemiological analysis
R-cran-epibasix: GNU R Elementary Epidemiological Functions
R-cran-epicalc: GNU R Epidemiological calculator
R-cran-epiestim: GNU R estimate time varying reproduction numbers from rpidemic curves
R-cran-epir: GNU R Functions for analysing epidemiological data
R-cran-epitools: GNU R Epidemiology Tools for Data and Graphics
R-cran-incidence: GNU R compute, handle, plot and model incidence of dated events
R-cran-kernelheaping: GNU R kernel density estimation for heaped and rounded data
R-cran-lexrankr: extractive summarization of text with the LexRank algorithm
R-cran-prevalence: GNU R tools for prevalence assessment studies
R-cran-seroincidence: GNU R seroincidence calculator tool
R-cran-sf: Simple Features for R
R-cran-sjplot: GNU R data visualization for statistics in social science
R-cran-surveillance: GNU R package for the Modeling and Monitoring of Epidemic Phenomena

Official Debian packages with lower relevance

Python3-epimodels: simple interface to simulate mathematical epidemic models in Python3
R-cran-cmprsk: GNU R subdistribution analysis of competing risks
R-cran-msm: GNU R Multi-state Markov and hidden Markov models in continuous time
Shiny-server: put Shiny web apps online

Packaging has started and developers might try the packaging code in VCS

Chime: COVID-19 Hospital Impact Model for Epidemics
Epifire: model the spread of an infectious disease in a population
Netepi-analysis: network-enabled tools for epidemiology and public health practice
Netepi-collection: network-enabled tools for epidemiology and public health practice
R-cran-covid19: GNU R Coronavirus COVID-19 data acquisition and visualization
Ushahidi: web platform for information collection

No known packages available but some record of interest (WNPP bug)

Repast: framework for creating agent based simulations

Hospital information systems - Debian Med suggestions for Hospital Information Systems

This metapackage contains dependencies for software and that could be useful ro run a Hospital Information System. While there is continuous work going on to package a ready to install system currently only preconditions are finished but hopefully helpful in hospitals anyway.

Official Debian packages with high relevance

Fis-gtm: metapackage for the latest version of FIS-GT.M database
Orthanc-wsi: Whole-slide imaging support for Orthanc (digital pathology)

Packaging has started and developers might try the packaging code in VCS

Care2x: integrated hospital information system
Openmrs: enterprise electronic medical record system framework
Tryton-modules-health: Tryton Application Platform (Health Module)
Vista-foia: metapackage for the latest version of vista-foia.

Unofficial packages built by somebody else

Oscar-mcmaster: Oscar (Web) A medical web application for electronic medical records

No known packages available but some record of interest (WNPP bug)

World-vista: repackage and extended version of VistA produced by WorldVistA

No known packages available

Hkma-cms: clinic management system
Ipath: telemedicine platform
Openeyes: ophthalmology electronic patient record system
Openmaxims: patient administration system and electronic patient record
Patientos: Healthcare Information System (HIS) for small hospitals and clinics

Imaging - Debian Med image processing and visualization packages

This metapackage will install Debian packages which might be useful in medical image processing and visualization.

On one hand, it installs several packages supporting various image file formats and image management, like DICOM (Digital Imaging and Communications in Medicine) which is the de-facto standard for medical image management, and NIFTI. On the other hand, it provides a variety of software packages that can be used for visualization and for image processing - either from a graphical user interface, the command line, or implemented in workflows.

Official Debian packages with high relevance

Amide: software for Medical Imaging
Ants: advanced normalization tools for brain and image analysis
Bart: tools for computational magnetic resonance imaging
Bart-view: viewer for multi-dimensional complex-valued data
Biosig-tools: format conversion tools for biomedical data formats
Camitk-imp: workbench application for the CamiTK library
Caret: Computerized Anatomical Reconstruction and Editing Toolkit
Conquest-common: ConQuest DICOM Server - common files
Ctn: Central Test Node, a DICOM implementation for medical imaging
Ctsim: Computed tomography simulator
Dcm2niix: next generation DICOM to NIfTI converter
Dcmtk: OFFIS DICOM toolkit command line utilities
Dicom3tools: DICOM medical image files manipulation and conversion tools
Dicomnifti: converts DICOM files into the NIfTI format
Dicomscope: OFFIS DICOM Viewer
Fslview: viewer for (f)MRI and DTI data
Gdf-tools: IO library for the GDF -- helper tools
Ginkgocadx: Medical Imaging Software and complete DICOM Viewer
Gwyddion: Scanning Probe Microscopy visualization and analysis tool
Heudiconv: DICOM converter with support for structure heuristics
Imagej: Image processing program with a focus on microscopy images
Imagevis3d: desktop volume rendering application for large data
Invesalius: 3D medical imaging reconstruction software
Ismrmrd-tools: command-line tools for ISMRMRD
Itksnap: semi-automatic segmentation of structures in 3D images
King: interactive system for three-dimensional vector graphics
Libgdcm-tools: Grassroots DICOM tools and utilities
Medcon: Medical Image (DICOM, ECAT, ...) conversion tool
Mia-tools: Command line tools for gray scale image processing
Mia-viewit: ??? missing short description for package mia-viewit :-(
Mialmpick: Tools for landmark picking in 3D volume data sets
Minc-tools: MNI medical image format tools
Mricron: magnetic resonance image conversion, viewing and analysis
Mrtrix3: diffusion-weighted MRI white matter tractography
Nifti-bin: tools shipped with the NIfTI library
Odil: C++11 library for the DICOM standard (application)
Odin: develop, simulate and run magnetic resonance sequences
Openslide-tools: Manipulation and conversion tools for OpenSlide
Orthanc: Lightweight, RESTful DICOM server for medical imaging
Orthanc-wsi: Whole-slide imaging support for Orthanc (digital pathology)
Pixelmed-apps: DICOM implementation containing Image Viewer and a ECG Viewer - cli
Plastimatch: medical image reconstruction and registration
Python3-dipy: Python library for the analysis of diffusion MRI datasets
Python3-nibabel: Python3 bindings to various neuroimaging data formats
Python3-nipy: Analysis of structural and functional neuroimaging data
Python3-nipype: Neuroimaging data analysis pipelines in Python3
Python3-nitime: timeseries analysis for neuroscience data (nitime)
Python3-pydicom: DICOM medical file reading and writing (Python 3)
Python3-pyxid: interface for Cedrus XID and StimTracker devices
Python3-surfer: visualize Freesurfer's data in Python3
Sigviewer: GUI viewer for biosignals such as EEG, EMG, and ECG
Sofa-apps: GUI for the Simulation Open Framework Architecture (SOFA)
Teem-apps: Tools to process and visualize scientific data and images - command line tools
Tifffile: Read and write image data from and to TIFF files
Voxbo: processing, statistical analysis, and display of brain imaging data
Vrrender: DICOM viewer
Vtk-dicom-tools: DICOM for VTK - tools
Xmedcon: Medical Image (DICOM, ECAT, ...) conversion tool (GUI)

Official Debian packages with lower relevance

Cmtk: Computational Morphometry Toolkit
Connectomeviewer: Interactive Analysis and Visualization for MR Connectomics
Conquest-dbase: ConQuest DICOM Server - DBaseIII backend
Conquest-mysql: ConQuest DICOM Server - MySQL backend
Conquest-postgres: ConQuest DICOM Server - PostgreSQL backend
Conquest-sqlite: ConQuest DICOM Server - SQLite backend
Elastix: toolbox for rigid and nonrigid registration of images
Illustrate: cartoonish representations of large biological molecules
Imagemagick: image manipulation programs -- binaries
Imview: Image viewing and analysis application
Orthanc-dicomweb: Plugin to extend Orthanc with support of WADO and DICOMweb
Orthanc-gdcm: DICOM transcoder/decoder for Orthanc using GDCM (notably for JPEG2k)
Orthanc-imagej: ImageJ plugin to import images from Orthanc
Orthanc-mysql: Plugins to use MySQL or MariaDB as a database back-end to Orthanc
Orthanc-neuro: Neuroimaging plugin for Orthanc
Orthanc-postgresql: Plugins to use PostgreSQL as a database back-end to Orthanc
Orthanc-webviewer: Web viewer of medical images for Orthanc
Paraview: Parallel Visualization Application
Pngquant: PNG (Portable Network Graphics) image optimising utility
Science-workflow: workflow management systems useful for scientific research
Trimage: GUI and command-line interface to optimize image files

Debian packages in contrib or non-free

Bart-cuda: tools for computational magnetic resonance imaging
Fsl: transitional dummy package
Vmtk: the Vascular Modeling Toolkit

Packaging has started and developers might try the packaging code in VCS

Bioimagesuite: integrated image analysis software suite
Bioimagexd: Analyzing, processing and visualizing of multi dimensional microscopy images
Cellprofiler: quantitatively measure phenotypes from images automatically
Crea: base library of the creaTools medical image processing suite
Dicoogle: Java Advanced Imaging API reference implementation
Fiji: "batteries-included" distribution of ImageJ
Freesurfer: analysis and visualization of functional brain imaging data
Incf-nidash-oneclick-clients: utility for pushing DICOM data to the INCF datasharing server
Insightapplications: InsightToolKit (ITK) based medical imaging applications
Jist: Java Image Science Toolkit
Kradview: medical image viewer for DICOM images
Libdcm4che-java: Clinical Image and Object Management
Mayam: Cross-platform DICOM Viewer
Micromanager: Microscopy Software
Mipav: quantitative analysis and visualization of medical images
Mni-colin27-nifti: Talairach stereotaxic space template
Openelectrophy: data analysis GUI for intra- and extra-cellular recordings
Openmeeg-tools: openmeeg library -- command line tools
Slicer: software package for visualization and image analysis - main application
Stabilitycalc: evaluate fMRI scanner stability
Via-bin: tools for volumetric image analysis
Visit: interactive parallel visualization and graphical analysis tool
Xnat: platform for data management and productivity tasks in neuroimaging

Unofficial packages built by somebody else

Cdmedicpacs: web interface to PACS to access DICOM study images
Mni-autoreg: MNI average brain (305 MRI) stereotaxic registration model
Mni-n3: MNI Non-parametric Non-uniformity Normalization
Opendicom.net: API to DICOM in C# for Mono

No known packages available but some record of interest (WNPP bug)

Devide: Delft Visualization and Image processing Development Environment
Dtitk: DTI spatial normalization and atlas construction toolkit
Eeglab: toolbox for processing and visualization of electrophysiological data
Isis: I/O framework for neuroimaging data
Jemris: high performance computing MRI simulator
Opensourcepacs: medical image referral, archiving, routing and viewing system

No known packages available

Blox: medical imaging and visualization program
Brainvisa: image processing factory for MR images
Dcm4chee: Clinical Image and Object Management (enterprise)
Dicom4j: Java framework for Dicom
Drjekyll: interactive voxel editor for viewing and editing three-dimensional images
Dti-query: dynamic queries of the white matter brain pathways
Ecg2png: convert scanned electrocardiograms into PNG format
Gimias: Graphical Interface for Medical Image Analysis and Simulation
Hid: database management system for clinical imaging
Maris: package suite for Radiological Workflow
Medisnap: photograph, manage, view, compare, document and archive medical photos
Mesa-test-tools: IHE Test Software for Radiology
Miview: Medical Images viewer and converter
Mni-icbm152-nlin-2009: MNI stereotaxic space human brain template
Mrisim: simulator for magnetic resonance imaging data
Omero: coming standard LIMS for microscopy images
Piano: medical image processing library for surgical planning
Pymeg: suite for analysis of magnetoencephalography (MEG) data
Stir: Software for Tomographic Image Reconstruction
Tempo: 3D visualization of brain electrical activity

Imaging development - Debian Med image processing and visualization packages development

This metapackage will install Debian packages which might be useful for developing applications for medical image processing and visualization.

Official Debian packages with high relevance

Cimg-dev: powerful image processing library
Ctn-dev: Development files for Central Test Node, a DICOM implementation
Gmic: GREYC's Magic for Image Computing
Libbart-dev: Development files for BART
Libbiosig-dev: I/O library for biomedical data - development files
Libcamitk-dev: Computer Assisted Medical Intervention Tool Kit - development
Libcifti-dev: development files for CiftiLib
Libedf-dev: European Data Format library - devel
Libgdcm2-dev: Grassroots DICOM development libraries and headers
Libgdf-dev: IO library for the GDF -- development library
Libgiftiio-dev: IO library for the GIFTI cortical surface data format - headers
Libinsighttoolkit5-dev: Image processing toolkit for registration and segmentation - development
Libismrmrd-dev: development files for ISMRMRD
Libmaxflow-dev: Development files for the maxflow-mincut algorithm
Libmdc2-dev: Medical Image (DICOM, ECAT, ...) conversion tool (development)
Libmia-2.4-dev: library for 2D and 3D gray scale image processing, development files
Libmialm-dev: Development files for the MIA landmark library
Libminc-dev: MNI medical image format development environment
Libnifti2-dev: IO libraries for the NIfTI-1 data format (development)
Libodil-dev: C++11 library for the DICOM standard (development files)
Libopencv-dev: development files for opencv
Libopenigtlink-dev: Open IGT Link is a simple network protocol - development
Libopenslide-dev: Development files for the OpenSlide library
Libpapyrus3-dev: DICOM compatible file format library
Libsight-dev: Sight header files
Libteem-dev: Tools to process and visualize scientific data and images - development
Libvigraimpex-dev: development files for the C++ computer vision library
Libvistaio-dev: Development files for the libvistaio library
Libvolpack1-dev: fast volume rendering library (development package)
Libvtk-dicom-dev: DICOM for VTK - dev
Libvtk9-dev: VTK header files
Libxdf-dev: C++ library for loading XDF files (headers and static lib)
Octave-bart: Octave bindings for BART
Octave-dicom: manipulate DICOM files in Octave
Octave-gdf: IO library for the GDF -- Octave interface
Odin: develop, simulate and run magnetic resonance sequences
Python3-biosig: Python3 bindings for BioSig library
Python3-bioxtasraw: process biological small angle scattering data
Python3-brian: simulator for spiking neural networks
Python3-dcmstack: DICOM to NIfTI conversion - python3 package
Python3-dipy: Python library for the analysis of diffusion MRI datasets
Python3-gdcm: Grassroots DICOM Python bindings
Python3-imageio: library for reading and writing image data (Python 3)
Python3-mia: Python-3 bindings for the MIA image processing library
Python3-mne: Python modules for MEG and EEG data analysis
Python3-nibabel: Python3 bindings to various neuroimaging data formats
Python3-nipy: Analysis of structural and functional neuroimaging data
Python3-nipype: Neuroimaging data analysis pipelines in Python3
Python3-nitime: timeseries analysis for neuroscience data (nitime)
Python3-openslide: Python 3 wrapper for reading whole slide image files
Python3-pydicom: DICOM medical file reading and writing (Python 3)
Python3-pyxnat: Interface to access neuroimaging data on XNAT servers
Python3-torchvision: Datasets, Transforms and Models specific to Computer Vision
Python3-vigra: Python3 bindings for the C++ computer vision library
R-cran-rniftilib: GNU/R interface to NIFTICLIB

Official Debian packages with lower relevance

Libcamp-dev: C++ multi-purpose reflection library (development files)
Libeegdev-dev: Biosignal acquisition device library (Development files)
Libfreeimage-dev: Support library for graphics image formats (development files)
Libics-dev: Image Cytometry Standard file reading and writing (devel)
Liblimereg-dev: Library for lightweight image registration [development files]
Libnifti-doc: NIfTI library API documentation
Libxdffileio-dev: Library to read/write EEG data file formats (development files)
Tifffile: Read and write image data from and to TIFF files

Debian packages in contrib or non-free

Libvmtk-dev: shared links and header files for vmtk
Python-vmtk: Python interface for vmtk

Packaging has started and developers might try the packaging code in VCS

Emokit: Emotiv EPOC headset Python interface
Libbio-formats-java: reading and writing proprietary microscopy image data and metadata
Libctk-dev: toolkit for medical imaging application development - devel
Libopenmeeg-dev: openmeeg library -- development files
Libopenslide-java: java wrapper for reading whole slide image files
Libvia-dev: library for volumetric image analysis

Unofficial packages built by somebody else

Libmni-perllib-perl: The MNI Perl Library

Laboratory - Debian Med suggestions for medical laboratories

This metapackage contains dependencies for software and that could be useful ro run a medical laboratory.

Official Debian packages with high relevance

Opencfu: count cell colonies (CFUs) on agar plates by processing digital pictures
Orthanc-wsi: Whole-slide imaging support for Orthanc (digital pathology)

Packaging has started and developers might try the packaging code in VCS

Openfreezer: Laboratory analysis, research and investigation software application

No known packages available

Catissuesuite: tool for biospecimen inventory management
Openelis: Enterprise Laboratory Information System

Oncology - Debian Med packages for oncology

This metapackage will install tools that are useful for radiation oncology.

Official Debian packages with high relevance

Orthanc-wsi: Whole-slide imaging support for Orthanc (digital pathology)
Simrisc: simulation model for breast/lung cancer risk

Official Debian packages with lower relevance

Python3-dicompylercore: core radiation therapy modules for DICOM / DICOM RT used by dicompyler

Packaging has started and developers might try the packaging code in VCS

Uw-prism: software tools for radiation therapy planning

No known packages available

Planunc: tools for radiotherapy treatment planning

Pharmacology - Debian Med packages for pharmaceutical research

This metapackage contains dependencies for a collection of software and documentation which is useful for pharmaceutical research.

Official Debian packages with high relevance

Chemtool: chemical structures drawing program
R-cran-dosefinding: Planning and Analyzing Dose Finding experiments
R-cran-rpact: Confirmatory Adaptive Clinical Trial Design and Analysis

Debian packages in contrib or non-free

Raccoon: preparation of in silico drug screening projects

Physics - Debian Med packages for medical physicists

This metapackage contains dependencies for a collection of software and documentation which is useful for medical physicists in radiation oncology, diagnostics imaging and related fields.

Official Debian packages with high relevance

Biosig-tools: format conversion tools for biomedical data formats
Gdf-tools: IO library for the GDF -- helper tools
Octave: GNU Octave language for numerical computations
Paw: Physics Analysis Workstation - a graphical analysis program
Paw++: Physics Analysis Workstation (Lesstif-enhanced version)
R-base: GNU R statistical computation and graphics system

Official Debian packages with lower relevance

Libbiosig-dev: I/O library for biomedical data - development files
Octave-biosig: Octave bindings for BioSig library
Paw-demos: Physics Analysis Workstation examples and tests
Python3-biosig: Python3 bindings for BioSig library
Python3-multipletau: multiple-tau algorithm for Python3/NumPy

No known packages available but some record of interest (WNPP bug)

Gate: Geant4 Application for Emission Tomography
Openvibe: platform for the design, test and use of BCI

Practice - Debian Med packages for practice management

This metapackage contains dependencies for a collection of software which might be helpful for practitioners to manage their practice.

Official Debian packages with high relevance

Entangle: Tethered Camera Control & Capture
Freediams: pharmaceutical drug prescription and interaction manager
Freemedforms-emr: electronic medical record manager
Ginkgocadx: Medical Imaging Software and complete DICOM Viewer
Gnumed-client: medical practice management - Client
Gnumed-server: medical practice management - server
Libchipcard-tools: tools for accessing chipcards
Orthanc: Lightweight, RESTful DICOM server for medical imaging
Orthanc-wsi: Whole-slide imaging support for Orthanc (digital pathology)
Oscar: Open Source CPAP Analysis Reporter (OSCAR)
Qrisk2: cardiovascular disease risk calculator
R-cran-medadherence: GNU R Medication Adherence: Commonly Used Definitions

Official Debian packages with lower relevance

Libctapimkt1: Read German Krankenversichertenkarte and eGK

Packaging has started and developers might try the packaging code in VCS

Freeshim: opensource electronic medical device interface
Openemr: Comprehensive medical practice management
Thera-pi: organization and management of outpatient clinics and rehabilitation-medicine companies

Unofficial packages built by somebody else

Elementalclinic: Electronical Medical Health record system for mental health
Freemed: Electronic Medical Record and Practice Management system
Tinyheb: billing system for midwives

No known packages available but some record of interest (WNPP bug)

Elexis: medical practice managemant system for use in Switzerland
Openrep: software for homeopathic repertorization and viewing materia medicae

No known packages available

Clearhealth: Medical practice management system
Freeb: Medical Bill formating module
Medintux: Medical practice management system
Mirrormed: EHR and practice management system
Mirth: HL7 integration engine
Openpms: medical billing, scheduling, and account management system
Proteus: clinical decision support guidelines model
Remitt: preparing and submitting medical billing data
Resmedicinae: comprising software solution for use in medicine
Sqlclinic: intranet solution for Saint Vincents Catholic Medical Centers of New York

Psychology - Debian Med packages for psychology

This metapackage contains dependencies for a collection of software which might be helpful for psychological research.

Official Debian packages with high relevance

Orthanc-neuro: Neuroimaging plugin for Orthanc
Praat: program for speech analysis and synthesis
Psignifit: Fitting and testing hypotheses about psychometric functions
Psychopy: environment for creating psychology stimuli in Python
Python3-bioxtasraw: process biological small angle scattering data
R-cran-foreign: GNU R package to read/write data from other stat. systems
R-cran-psy: GNU R procedures for psychometrics
R-cran-psych: GNU R procedures for psychological, psychometric, and personality research
R-cran-psychometric: GNU R applied psychometric theory
R-cran-psychotree: GNU R recursive partitioning based on psychometric models
R-cran-psyphy: functions for analyzing psychophysical data in GNU R

Official Debian packages with lower relevance

Python-pyepl: module for coding psychology experiments in Python
Python3-bids-validator: validator for the Brain Imaging Data Structure (BIDS) datasets
Python3-bmtk: development package for building, simulating and analysing large-scale networks
Python3-pynwb: Python library for working with Neurodata in the NWB format
Science-psychophysics: Debian Science packages for Psychophysics

Rehabilitation - Debian Med packages for rehabilitation technologies

This metapackage will install tools that are useful for rehabilitation and therapy.

Official Debian packages with high relevance

Sitplus: Free software framework for ludic-therapeutic activities

Official Debian packages with lower relevance

Aghermann: Sleep-research experiment manager

Research - Debian Med packages for medical research

This metapackage will install tools that are useful for medical research.

Official Debian packages with high relevance

R-cran-rpact: Confirmatory Adaptive Clinical Trial Design and Analysis

No known packages available but some record of interest (WNPP bug)

Openclinica: electronic data capture and clinical data management

Statistics - Debian Med statistics

This metapackage will install packages which are helpful to do statistics with a special focus on tasks in medical care.

Official Debian packages with high relevance

R-bioc-edger: Empirical analysis of digital gene expression data in R
R-bioc-limma: linear models for microarray data
R-bioc-multtest: Bioconductor resampling-based multiple hypothesis testing
R-bioc-qvalue: GNU R package for Q-value estimation for FDR control
R-cran-ade4: GNU R analysis of ecological data
R-cran-beeswarm: bee swarm plot, an alternative to stripchart
R-cran-pvclust: Hierarchical Clustering with P-Values via Multiscale Bootstrap
R-cran-randomforest: GNU R package implementing the random forest classificator
R-cran-rwave: GNU R time-frequency analysis of 1-D signals
R-cran-snowfall: GNU R easier cluster computing (based on snow)
R-cran-waveslim: GNU R wavelet routines for 1-, 2- and 3-D signal processing
R-cran-wavethresh: GNU R wavelets statistics and transforms

Official Debian packages with lower relevance

Science-statistics: Debian Science Statistics packages

Packaging has started and developers might try the packaging code in VCS

Rstudio: GNU R IDE

Tools - Debian Med several tools

This metapackage will install tools for several purposes in health care. Currently it contains some simple programs for Personal Health.

Official Debian packages with high relevance

Cronometer: CRON-o-Meter - Exercise and nutrient intake tracker
Cycle: calendar program for women
Edfbrowser: viewer for biosignal storage files such as bdf and edf
Galileo: Utility to securely synchronize a Fitbit device with the Fitbit web service
Hunspell-de-med: German medical dictionary for hunspell
Hunspell-en-med: English medical dictionary for hunspell
Nut-nutrition: dietary nutrition analysis software
Nutsqlite: Dietary nutrition analysis software
Pcalendar: track menstrual cycles and predict fertility periods
Pondus: personal weight manager for GTK+2
Python3-fitbit: FitBit REST API Client Implementation - Python 3
Quitcount: Small tool which may help yourself quit smoking
R-cran-fitbitscraper: Import your Fitbit data from the Fitbit's website into R
R-cran-fitcoach: R package for analysis and retrieve data of Fitbit
Wgerman-medical: German medical dictionary words for /usr/share/dict
Workrave: Repetitive Strain Injury prevention tool

Official Debian packages with lower relevance

Entangle: Tethered Camera Control & Capture
Goldencheetah: set of analysis tools for cycling performance
Mencal: menstruation calendar
Oscar: Open Source CPAP Analysis Reporter (OSCAR)

Debian packages in contrib or non-free

Mssstest: Normalisation of disease scores for patients with Multiple Sclerosis

Packaging has started and developers might try the packaging code in VCS

Pesco: Cognitive stimulation tool for elderly or cognitively impaired

Typesetting - Debian Med support for typesetting and publishing

This metapackage will install Debian packages that might be helpful for typesetting and publishing in medical care and structural biology.

Official Debian packages with high relevance

King: interactive system for three-dimensional vector graphics
Texlive-latex-extra: TeX Live: LaTeX additional packages
Texlive-science: TeX Live: Mathematics, natural sciences, computer science packages

Official Debian packages with lower relevance

Biber: Much-augmented BibTeX replacement for BibLaTeX users
Bibus: bibliographic database
Jabref-plugin-oo: LibreOffice plugin for JabRef (transitional dummy package)
Kbibtex: BibTeX editor for KDE
R-cran-qqman: R package for visualizing GWAS results using Q-Q and manhattan plots

Tasks page

Table of contents

Official Debian packages with high relevance

Official Debian packages with lower relevance

Debian packages in contrib or non-free

Debian packages in New queue (hopefully available soon)

Packaging has started and developers might try the packaging code in VCS

Unofficial packages built by somebody else

No known packages available but some record of interest (WNPP bug)

No known packages available

Official Debian packages with high relevance

Official Debian packages with lower relevance

Debian packages in contrib or non-free

Packaging has started and developers might try the packaging code in VCS

No known packages available

Official Debian packages with high relevance

Official Debian packages with lower relevance

Debian packages in contrib or non-free

Packaging has started and developers might try the packaging code in VCS

No known packages available

Official Debian packages with high relevance

Official Debian packages with lower relevance

Packaging has started and developers might try the packaging code in VCS

No known packages available but some record of interest (WNPP bug)

No known packages available

Official Debian packages with high relevance

Debian packages in contrib or non-free

Packaging has started and developers might try the packaging code in VCS

Packaging has started and developers might try the packaging code in VCS

No known packages available

Official Debian packages with high relevance

Official Debian packages with lower relevance

Debian packages in contrib or non-free

Debian packages in experimental

Packaging has started and developers might try the packaging code in VCS

Official Debian packages with high relevance

Official Debian packages with lower relevance

No known packages available

Official Debian packages with high relevance

Official Debian packages with high relevance

Official Debian packages with lower relevance

Packaging has started and developers might try the packaging code in VCS

No known packages available but some record of interest (WNPP bug)

Official Debian packages with high relevance

Packaging has started and developers might try the packaging code in VCS

Unofficial packages built by somebody else

No known packages available but some record of interest (WNPP bug)

No known packages available

Official Debian packages with high relevance

Official Debian packages with lower relevance

Debian packages in contrib or non-free

Packaging has started and developers might try the packaging code in VCS

Unofficial packages built by somebody else

No known packages available but some record of interest (WNPP bug)

No known packages available

Official Debian packages with high relevance

Official Debian packages with lower relevance

Debian packages in contrib or non-free

Packaging has started and developers might try the packaging code in VCS

Unofficial packages built by somebody else

Official Debian packages with high relevance

Packaging has started and developers might try the packaging code in VCS

No known packages available

Official Debian packages with high relevance

Official Debian packages with lower relevance

Packaging has started and developers might try the packaging code in VCS

No known packages available

Official Debian packages with high relevance

Debian packages in contrib or non-free

Official Debian packages with high relevance

Official Debian packages with lower relevance

No known packages available but some record of interest (WNPP bug)

Official Debian packages with high relevance

Official Debian packages with lower relevance

Packaging has started and developers might try the packaging code in VCS

Unofficial packages built by somebody else

No known packages available but some record of interest (WNPP bug)

No known packages available

Official Debian packages with high relevance

Official Debian packages with lower relevance