Debian Med Cloud packages

ABySS is a de novo, parallel, sequence assembler that is designed for short reads. It may be used to assemble genome or transcriptome sequence data. Parallelization is achieved using MPI, OpenMP and pthread.

本パッケージは acedb がその Makefile の 'other' ターゲット以下に集めた 全ての小さなアプリケーションを集めたものです。

efetch: おそらく 'entry fetch' の略で、配列情報を一般的 DNA およびタンパク質 データベースから配列情報を取得します。

Aevol is a digital genetics model: populations of digital organisms are subjected to a process of selection and variation, which creates a Darwinian dynamics.

By modifying the characteristics of selection (e.g. population size, type of environment, environmental variations) or variation (e.g. mutation rates, chromosomal rearrangement rates, types of rearrangements, horizontal transfer), one can study experimentally the impact of these parameters on the structure of the evolved organisms. In particular, since Aevol integrates a precise and realistic model of the genome, it allows for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences).

The simulation platform comes along with a set of tools for analysing phylogenies and measuring many characteristics of the organisms and populations along evolution.

Alien_hunter は、Interpolated Variable Order Motifs (IVOMs)の実装により、 遺伝子の水平伝播 (HGT) イベントの推定するためのアプリケーションです。 IVOM アプローチでは、可変順序モチーフ分布により組成上のバイアスを利用して、 固定順序法に比べてシーケンスのローカル組成物をより確実にキャプチャします。 必要に応じて予測は、変化点検出フレームワーク内で 2 ステート 2 次隠れマルコフ モデル (HMM) で解析することができ、予測領域の境界の局在を最適化することが できます。予測 (embl 形式) は、http://www.sanger.ac.uk/Software/Artemis/ より自由に利用できる Artemis ゲノムビューアへ自動的にロードすることが できます。

ALTree was designed to perform association detection and localization of susceptibility sites using haplotype phylogenetic trees: first, it allows the detection of an association between a candidate gene and a disease, and second, it enables to make hypothesis about the susceptibility loci.

AMAP is a command line tool to perform multiple alignment of peptidic sequences. It utilizes posterior decoding, and a sequence-annealing alignment, instead of the traditional progressive alignment method. It is the only alignment program that allows one to control the sensitivity / specificity tradeoff. It is based on the ProbCons source code, but uses alignment metric accuracy and eliminates the consistency transformation.

The Java visualisation tool of AMAP 2.2 is not yet packaged in Debian.

AmpliconNoise is a package of applications to clean up high-throughput sequence data. It consists of three main parts:

Pyronoise - does flowgram-based clustering to spot misreads SeqNoise - removes PCR point mutations Perseus - removes PCR chimeras without the need for a set of reference sequences

Previously there was a standalone "Pyronoise" by the same authors and this package includes an updated version. There is also a "Denoiser" in Qiime which is related but distinct.

Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes more after BLAST/BLAT. It's most useful for the alignment of sequencing reads where the DNA sequence is somehow modified (think ancient DNA or bisulphite treatment) and/or there is more divergence between sample and reference than what fast mappers will handle gracefully (say the reference genome is missing and a related species is used instead).

The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base-paired cloverleaf. tmRNA genes are identified using a modified version of the BRUCE program.

ARDEN (Artificial Reference Driven Estimation of false positives in NGS data) is a novel benchmark that estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It allows the computation of error rates specifically for a dataset and the construction of a ROC-curve. Thereby, it can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation.

AutoDock は、かなり小さいリガンド化学物質がかなり大きな受容体タンパク質への ドッキングする様子のシミュレーションを処理するプログラム群の代表パッケージ です。以前のバージョンでは、配位子はすべての柔軟性を持っているのに対して、 タンパク質は比較的剛直でした。この最新バージョン 4 は、表面残基の側鎖を選択 して柔軟性を持たせることができます。すなわち、回転異性体を考慮に入れること ができます。

AutoDock プログラムは、ターゲットタンパク質を記述するグリッド・セットへのリ ガンドの結合を処理します。このグリッドは AutoGrid により事前に計算されます。

AutoDock Vina is a program to support drug discovery, molecular docking and virtual screening of compound libraries. It offers multi-core capability, high performance and enhanced accuracy and ease of use.

The same institute also developed autodock, which is widely used.

O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461

AutoDockSuite は、三次元構造のわかっている受容体へ、より小さな化学物質がど のようにドッキングするかを分子レベルで解析できます。

AutoGrid プログラムは、リガンドのドッキングを計算するため、タンパク質が点電 荷に与える影響を記述するようなグリッド・セットを事前計算します。この力がリ ガンドに与える影響は、AutoDock プログラムにより解析します。

BamTools は、BAM ファイルを用いた研究解析とデータ管理を支援します。 現行のシーケンシング技術により生成された、通常圧縮されたバイナリフォーマット で格納されており、生物情報学研究に通常用いられているテキストベースの パーサーでは容易に扱うことのできない、莫大なデータを扱えます。

BamTools は BAM ファイルサポート用の C++ API と コマンドラインツールの 両方を提供します。

これは bamtools コマンドラインツールキットです。

使用可能な bamtools コマンド:

 convert  BAM とその他多数のフォーマットとの間の変換
 count    BAM ファイル内のアラインメント数を表示
 coverage 入力 BAM ファイルからカバレッジ統計を表示
 filter   ユーザー定義の基準にしたがって BAM ファイルをフィルタリング
 header   BAM ヘッダ情報を表示
 index    BAM ファイルのインデックスを生成
 merge    複数の BAM ファイルを一つにマージ
 random   既存の BAM ファイルからランダムなアラインメントを選択
          （テストツールなど用）
 resolve  ペアエンドリードを解決（必要に応じて IsProperPair フラグをセット）
 revert   重複マークを削除して元のベース品質を復元
 sort     BAM ファイルをなんらかの基準に従ってソート
 split    ユーザー定義のプロパティで BAM ファイルを分割し、各値が見付かる
          ごとに新しい出力 BAM ファイルを作成
 stats    入力 BAM ファイルから基本的統計を表示

The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by streaming several BEDTools together.

The groupBy utility is distributed in the filo package.

The Bioperl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules. It is well-accepted throughout the community and used in many high-profile projects, e.g., Ensembl.

The recommended packages are needed to run some of the included binaries, for a detailed explanation including the specific Perl modules please see README.Debian.

The suggested package enhances the manual pages.

Contains scripts from the BioPerl-Run package. This package will also install all wrappable applications packaged in Debian. The ones that are not Free are "Suggested" by this package.

SQUID is a library of C code functions for sequence analysis. It also includes a number of small utility programs to convert, show statistics, manipulate and do other functions on sequence files.

The original name of the package is "squid", but since there is already a squid on the archive (a proxy cache), it was renamed to "biosquid".

This package contains some tools to demonstrate the features of the SQUID library.

This is a transitional dummy package for ncbi-blast+-legacy. It can safely be removed.

This package addresses the problem to interpret the results from the latest (2010) DNA sequencing technologies. Those will yield fairly short stretches and those cannot be interpreted directly. It is the challenge for tools like Bowtie to give a chromosomal location to the short stretches of DNA sequenced per run.

Bowtie aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.

Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes

Boxshade はマルチプルアライメントされたタンパク質または DNA 配列のきれいな プリントアウトを生成するプログラムです。このプログラム自身はアライメントを 行いませんので、入力ファイルとして、マルチプルアライメントプログラムが作成 したか、または個々のツールで手動編集したファイルが必要です。

Boxshade はマルチプルアライメントされた配列を PILEUP-MSF, CLUSTAL-ALN, MALIGNED-data および ESEE-save ファイルから読み込みます (最大 150 配列 まで、各配列は最大 10000 エレメントまでの制限があります) 。各種シェーディ ングを一致する/類似の残基に適用できます。出力は画面に表示するか、または以下の フォーマットによりファイルに出力できます: ANSI/VT100, PS/EPS, RTF, HPGL, ReGIS, LJ-250-printer, ASCII, xFIG, PICT, HTML

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

Cassiopee index and search library C implementation. It is a complete rewrite of the ruby Cassiopee gem. It scans an input genomic sequence (dna/rna/protein) and search for a subsequence with exact match or allowing substitutions (Hamming distance) and/or insertion/deletions.

This package contains the cassiopee and cassiopeeknife tools.

cd-hit contains a number of programs designed to quickly group sequences. cd-hit groups proteins into clusters that meet a user-defined similarity threshold. cd-hit-est is similar to cd-hit, but designed to group nucleotide sequences (without introns). cd-hit-est-2d is similar to cd-hit-2d but designed to compare two nucleotide datasets. A number of other related programs are also in this package. Please see the cd-hit user manual, also part of this package, for further information.

CDB (Constant DataBase) can be used for creating indices for quick retrieval of any particular sequences from large multi-FASTA files. It has the option to compress data records in order to save space.

Circos は円状レイアウトでデータを可視化します。オブジェクトや位置の間の関係 性を明らかにするのに最適で、情報のつまった出版品質の画像を作成することがで きます。

本パッケージは、(gnuplot に似た) コマンドライン駆動で、完全スクリプト可能な Circos プロットエンジンを提供します。

Clearcut is the reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm by J. Evans, L. Sheneman, and J. Foster from the Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.

ClonalFrame はサンプル中のメンバー間のクローン関係を同定します。また、 クローン継承を打ち切った染色体の相同組み換えイベントの位置を推定します。

ClonalFrame は DNA の単一フラグメントからゲノム全体まで、どんな種類の 配列データにも適用できます。7つの遺伝子フラグメントがシーケンシングされている MLST データの解析に最も適していますが、シーケンシングされた領域の長さと個数の 両方が増え、ゲノム全体までおよぶにつれて段階的により強力になっていきます。 しかし、配列はアラインされている必要があります。もしアラインされていないゲノム データをお持ちなら、バクテリアゲノム全体を ClonalFrame が必要とするまさに その形式でアラインしてくれる Mauve を利用することをお勧めします。

Clustal Omega is a general-purpose multiple sequence alignment (MSA) program, primarily for amino-acid sequences. It produces high quality MSAs and is capable of handling data sets of hundreds of thousands of sequences in reasonable time, using multiple processors where available.

This program performs an alignment of multiple nucleotide or amino acid sequences. It recognizes the format of input sequences and whether the sequences are nucleic acid (DNA/RNA) or amino acid (proteins). The output format may be selected from in various formats for multiple alignments such as Phylip or FASTA. Clustal W is very well accepted.

The output of Clustal W can be edited manually but preferably with an alignment editor like SeaView or within its companion Clustal X. When building a model from your alignment, this can be applied for improved database searches. The Debian package hmmer creates such in form of an HMM.

ConCavity predicts protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

ConCavity takes as input a PDB format protein structure and optionally files that characterize the evolutionary sequence conservation of the chains in the structure file.

The following result files are produced by default:

• Residue ligand binding predictions for each chain (*.scores).
• Residue ligand binding predictions in a PDB format file (residue scores placed in the temp. factor field, *_residue.pdb).
• Pocket prediction locations in a DX format file (*.dx).
• PyMOL script to visualize the predictions (*.pml).

This package provides score_conservation(1), a tool to score protein sequence conservation.

The following conservation scoring methods are implemented:

• sum of pairs
• weighted sum of pairs
• Shannon entropy
• Shannon entropy with property groupings (Mirny and Shakhnovich 1995, Valdar and Thornton 2001)
• relative entropy with property groupings (Williamson 1995)
• von Neumann entropy (Caffrey et al 2004)
• relative entropy (Samudrala and Wang 2006)
• Jensen-Shannon divergence (Capra and Singh 2007)

A window-based extension that incorporates the estimated conservation of sequentially adjacent residues into the score for each column is also given. This window approach can be applied to any of the conservation scoring methods.

The program accepts alignments in the CLUSTAL and FASTA formats.

The sequence-specific output can be used as the conservation input for concavity.

Conservation is highly predictive in identifying catalytic sites and residues near bound ligands.

GNU Datamash is a command-line program which performs basic numeric, textual and statistical operations on input textual data files. It is designed to be portable and reliable, and aid researchers to easily automate analysis pipelines, without writing code or even short scripts.

DIALIGN2 is a command line tool to perform multiple alignment of protein or DNA sequences. It constructs alignments from gapfree pairs of similar segments of the sequences. This scoring scheme for alignments is the basic difference between DIALIGN and other global or local alignment methods. Note that DIALIGN does not employ any kind of gap penalty.

DIALIGN-TX はタンパク質または DNA 配列のマルチプルアライメントを実行するた めのコマンドラインツールです。セグメントベースのアプローチの完全な再実装で あり、DIALIGN 2.2 や DIALIGN-T と比較して出力アライメントの品質を有意に向上 するいくつかの新たな改良や発見的手法を含んでいます。ペアワイズアライメント において、DIALIGN-TX は、低スコアの局所アライメントの連鎖を孤立した高スコア の断片より好む、断片連鎖アルゴリズムを使用します。マルチプルアライメントで は、偽の局所的な配列類似性に対する感度を落とすように改良された貪欲法を使用 します。

Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).

Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed.

The software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads, enhance the kissnp2 results by computing per read set and for each found SNP:

 1) its mean read coverage
 2) the (phred) quality of reads generating the polymorphism.

This program is superseded by DiscoSnp++.

'disulfinder' is for predicting the disulfide bonding state of cysteines and their disulfide connectivity starting from sequence alone. Disulfide bridges play a major role in the stabilization of the folding process for several proteins. Prediction of disulfide bridges from sequence alone is therefore useful for the study of structural and functional properties of specific proteins. In addition, knowledge about the disulfide bonding state of cysteines may help the experimental structure determination process and may be useful in other genomic annotation tasks.

'disulfinder' predicts disulfide patterns in two computational stages: (1) the disulfide bonding state of each cysteine is predicted by a BRNN-SVM binary classifier; (2) cysteines that are known to participate in the formation of bridges are paired by a Recursive Neural Network to obtain a connectivity pattern.

dnaclust is a tool for clustering large number of short DNA sequences. The clusters are created in such a way that the "radius" of each clusters is no more than the specified threshold.

The input sequences to be clustered should be in Fasta format. The id of each sequence is based on the first word of the seqeunce in the Fasta format. The first word is the prefix of the header up to the first occurrence of white space characters in the header.

DSSP is an application you use to assign the secondary structure of a protein based on its solved three dimensional (3D) structure.

This version (4.2) of DSSP is a rewrite that writes annotated mmCIF files by default but can still produce the older dssp format. New is also the support of PP helices.

The DOMAINATRIX programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.

Applications in the current domainatrix release are cathparse (generates DCF file from raw CATH files), domainnr (removes redundant domains from a DCF file), domainreso (removes low resolution domains from a DCF file), domainseqs (adds sequence records to a DCF file), domainsse (adds secondary structure records to a DCF file), scopparse (generates DCF file from raw SCOP files) and ssematch (searches a DCF file for secondary structure matches).

The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.

Applications in the current domalign release are allversusall (sequence similarity data from all-versus-all comparison), domainalign (generates alignments (DAF file) for nodes in a DCF file), domainrep (reorders DCF file to identify representative structures) and seqalign (extend alignments (DAF file) with sequences (DHF file)).

The DOMSEARCH programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.

Applications in this DOMSEARCH release are seqfraggle (removes fragment sequences from DHF files), seqnr (removes redundancy from DHF files), seqsearch (generates PSI-BLAST hits (DHF file) from a DAF file), seqsort (Remove ambiguous classified sequences from DHF files) and seqwords (Generates DHF files from keyword search of UniProt).

EMBOSS は、分子生物学のユーザコミュニティ (例: EMBnet) のために開発された オープンソースな解析用ソフトウェアパッケージです。このソフトウェアを 使うことで、様々なフォーマットで書かれたデータを自動的に処理したり、 ウェブから配列データを透過的に取得したりもできます。また、このパッケージには 拡張ライブラリが含まれているので、真のオープンソース精神に則って ソフトウェアを開発しリリースできるプラットフォームです。 さらに、EMBOSS は様々な配列解析用パッケージやツールとシームレスに 統合されています。EMBOSS は、長く続いた商用パッケージソフトウェアへの流れを 断ち切ったのです。

Exonerate allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. Much of the functionality of the Wise dynamic programming suite was reimplemented in C for better efficiency. Exonerate is an intrinsic component of the building of the Ensembl genome databases, providing similarity scores between RNA and DNA sequences and thus determining splice variants and coding sequences in general.

An In-silico PCR Experiment Simulation System (see the ipcress man page) is packaged with exonerate.

This package also comes with a selection of utilities for performing simple manipulations quickly on fasta files beyond 2Gb

fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML (part of his PHYLIP package). Users should consult the documentation for DNAML before using this program.

fastDNAml is an attempt to solve the same problem as DNAML, but to do so faster and using less memory, so that larger trees and/or more bootstrap replicates become tractable. Much of fastDNAml is merely a recoding of the PHYLIP 3.3 DNAML program from PASCAL to C.

Note that the homepage of this program is not available any more and so this program will probably not see any further updates.

Genetic linkage analysis is a statistical technique used to map genes and find the approximate location of disease genes. There was a standard software package for genetic linkage called LINKAGE. FASTLINK is a significantly modified and improved version of the main programs of LINKAGE that runs much faster sequentially, can run in parallel, allows the user to recover gracefully from a computer crash, and provides abundant new documentation. FASTLINK has been used in over 1000 published genetic linkage studies.

This package contains the following programs:

 ilink:    GEMINI optimization procedure to find a locally
           optimal value of the theta vector of recombination
           fractions
 linkmap:  calculates location scores of one locus against a
           fixed map of other loci
 lodscore: compares likelihoods at locally optimal theta
 mlink:    calculates lod scores and risk with two of more loci
 unknown:  identify possible genotypes for unknowns

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

The main functions of FastQC are

• Import of data from BAM, SAM or FastQ files (any variant)
• Providing a quick overview to tell you in which areas there may be problems
• Summary graphs and tables to quickly assess your data
• Export of results to an HTML based permanent report
• Offline operation to allow automated generation of reports without running the interactive application

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It handles alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7.

FastTree is more accurate than PhyML 3 with default settings, and much more accurate than the distance-matrix methods that are traditionally used for large alignments. FastTree uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT (Jones-Taylor-Thornton 1992) model of amino acid evolution. To account for the varying rates of evolution across sites, FastTree uses a single rate for each site (the "CAT" approximation). To quickly estimate the reliability of each split in the tree, FastTree computes local support values with the Shimodaira-Hasegawa test (these are the same as PhyML 3's "SH-like local supports").

This package contains a single threaded version (fasttree) and a parallel version which uses OpenMP (fasttreMP).

Genome coverage, the number of sequencing reads mapped to a position in a genome, is an insightful indicator of irregularities within sequencing experiments. While the average genome coverage is frequently used within algorithms in computational genomics, the complete information available in coverage profiles (i.e. histograms over all coverages) is currently not exploited to its full extent. Thus, biases such as fragmented or erroneous reference genomes often remain unaccounted for. Making this information accessible can improve the quality of sequencing experiments and quantitative analyses.

fitGCP is a framework for fitting mixtures of probability distributions to genome coverage profiles. Besides commonly used distributions, fitGCP uses distributions tailored to account for common artifacts. The mixture models are iteratively fitted based on the Expectation-Maximization algorithm.

Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.

Parameter names changed in Flexbar. Please review scripts. The recent months, default settings were optimised, several bugs were fixed and various improvements were made, e.g. revamped command-line interface, new trimming modes as well as lower time and memory requirements.

FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011).

FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible.

A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.

jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example.

This package contains the command line tool freecontact(1).

One goal of sequencing based metagenomic analysis is the quantitative taxonomic assessment of microbial community compositions. However, the majority of approaches either quantify at low resolution (e.g. at phylum level) or have severe problems discerning highly similar species. Yet, accurate quantification on species level is desirable in applications such as metagenomic diagnostics or community comparison. GASiC is a method to correct read alignment results for the ambiguities imposed by similarities of genomes. It has superior performance over existing methods.

The GenomeTools contains a collection of useful tools for biological sequence analysis and -presentation combined into a single binary.

The toolkit contains binaries for sequence and annotation handling, sequence compression, index structure generation and access, annotation visualization, and much more.

A program to visualize the alignment of two genomic sequences together with their annotations. From GFF-format input files it produces PostScript figures for that alignment. The following menu lists many features of gff2aplot:

• Comprehensive alignment plots for any GFF-feature. Attributes are defined separately so you can modify only whatsoever attributes for a given file or share same customization across different data-sets.
• All parameters are set by default within the program, but it can be also fully configured via gff2ps-like flexible customization files. Program can handle several of such files, summarizing all the settings before producing the corresponding figure. Moreover, all customization parameters can be set via command-line switches, which allows users to play with those parameters before adding any to a customization file.
• Source order is taken from input files, if you swap file order you can visualize alignment and its annotation with the new input arrangement.
• All alignment scores can be visualized in a PiP box below gff2aplot area, using grey-color scale, user-defined color scale or score-dependent gradients.
• Scalable fonts, which can also be chosen among the basic PostScript default fonts. Feature and group labels can be rotated to improve readability in both annotation axes.
• The program is still defined as a Unix filter so it can handle data from files, redirections and pipes, writing output to standard-output and warnings to standard error.
• gff2aplot is able to manage many physical page formats (from A0 to A10, and more -see available page sizes in its manual-), including user-defined ones. This allows, for instance, the generation of poster size genomic maps, or the use of a continuous-paper supporting plotting device, either in portrait or landscape.
• You can draw different alignments on same alignment plot and distinguish them by using different colors for each.
• Shape dictionary has been expanded, so that further feature shapes are now available (see manual).
• Annotation projections through alignment plots (so called ribbons) emulate transparencies via complementary color fill patterns. This feature allows one to show color pseudo-blending when horizontal and vertical ribbons overlap.

gff2ps は gff 形式のレコードを PostScript による高品質な一次元プロットに 変換する目的で開発されたスクリプトプログラムです。このようなプロットは ゲノム構造を比較したり、ゲノムアノテーションプログラムの出力を可視化するのに 便利でしょう。 このプログラムは、GFF ファイル自身がフォーマット情報を十分に含むと仮定して いるため、とても単純な方法で使用できるのはもちろん、たくさんのオプションや 設定ファイルによる、自由度の大きなカスタマイズも可能となっています。

GIIRA is a gene prediction method that identifies potential coding regions exclusively based on the mapping of reads from an RNA-Seq experiment. It was foremost designed for prokaryotic gene prediction and is able to resolve genes within the expressed region of an operon. However, it is also applicable to eukaryotes and predicts exon intron structures as well as alternative isoforms.

GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. A motif is a re-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif. The main innovation of GLAM2 is that it allows insertions and deletions in motifs.

This package includes programs for discovering motifs shared by a set of sequences and finding matches to these motifs in a sequence database, as well as utilities for converting glam2 motifs to standard alignment formats, masking glam2 motifs out of sequences so that weaker motifs can be found, and removing highly similar members of a set of sequences.

The package includes these programs:

 glam2:       discovering motifs shared by a set of sequences;
 glam2scan:   finding matches, in a sequence database, to a motif discovered
              by glam2;
 glam2format: converting glam2 motifs to  standard alignment formats;
 glam2mask:   masking glam2 motifs out of sequences, so that weaker motifs
              can be found;
 glam2-purge: removing highly similar members of a set of sequences.

In this binary package, the fast Fourier algorithm (FFT) was enabled for the glam2 program.

This package contains the programs GMAP and GSNAP as well as utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning EST, mRNA and cDNA sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single-end and paired-end transcriptome reads. Both tools can use a database of

• known splice sites and identify novel splice sites.
• known single-nucleotide polymorphisms (SNPs). GSNAP can align bisulfite-treated DNA.

Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file.

Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, metaproteomic shotgun and amplicon datasets from current sequencing technologies such as Sanger, 454, Illumina. These simulated datasets can be used to test the accuracy of bioinformatic tools under specific hypothesis, e.g. with or without sequencing errors, or with low or high community diversity. Grinder may also be used to help decide between alternative sequencing methods for a sequence-based project, e.g. should the library be paired-end or not, how many reads should be sequenced.

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers.

This package contains variants both for execution on a single machine, and using the MPI interface across multiple machines.

HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

This package contains HHsearch and HHblits among other programs and utilities.

HHsearch takes as input a multiple sequence alignment (MSA) or profile HMM and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous proteins. HHsearch is often used for protein structure prediction to detect homologous templates and to build highly accurate query-template pairwise alignments for homology modeling.

HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and, using an iterative search strategy, adds significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments.

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome). Based on an extension of BWT for graphs a graph FM index (GFM) was designed and implementd. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).

HMMER は、プロファイル隠れマルコフモデル法の実装であり、多重配列アライメン トをクエリー (問い合わせ) として用いた生物学配列データベースの感度の高い検 索を行うためのものです。

入力として多重配列アライメントを与えると、HMMER は "隠れマルコフモデル" と 呼ばれる統計モデルを構築します。このモデルをさらにクエリーとして、配列デー タベースから、配列ファミリの追加のホモログ　(相同体) を検索する (またはアラ イメントする) ことができます。