Debian Med Phylogeny packages

ALTree wurde für entworfen, um Assoziationen zu entdecken und Suszeptibilitäts-Lokuse (susceptibility loci) mittels phylogenetischen Bäumen aus Haplotypen zu lokalisieren. Zum Einen ermöglicht sie die Entdeckung einer Assoziation zwischen einem untersuchten Gen und einer Krankheit, zum Anderen wird eine Hypothese über Suszeptibilitäts-Lokuse möglich.

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Included is a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

Clustal W führt ein Alignment mehrerer Nukleotid- oder Aminosäurensequenzen aus. Das Programm erkennt das Format der Eingabesequenzen und ob die Sequenzen aus Nuklein- (DNA/RNA) oder Aminosäuren (Proteine) bestehen. Das Ausgabeformat kann aus verschiedenen Formaten für multiple Alignments ausgewählt werden, etwa Phylip oder FASTA. Clustal W ist allgemein anerkannt.

Die Ausgabe von Clustal W kann händisch editiert werden, jedoch wird ein Alignment-Editor wie SeaView oder Clustal X empfohlen. Bei der Erstellung eines Modells aus Ihrem Alignment, kann die Ausgabe für verbesserte Datenbanksuchen verwendet werden. Das Debian-Paket hmmer erstellt dies mittels eines Hidden-Markov-Modells (HMM).

Dieses Paket enthält eine grafische Oberfläche für Clustal, ein Programm für multiple Sequenzalignments. Das Paket enthält für die Analyse der Resultate eine integrierte Umgebung für multiple Sequenz- und Profilalignments. Das Sequenzalignment wird in einem Fenster angezeigt. Es wurde ein vielseitiges Farbschema implementiert, um konservierte Teile des Alignments hervorzuheben. Für professionelle Präsentationen ist das LaTeX-Paket texshade oder boxshade besser geeignet.

Sie können alle Optionen für herkömmliche multiple Sequenz- und Profilaligments über Pull-Down-Menüs am oberen Rand des Fensters erreichen. Sie können Sequenzen ausschneiden und einfügen, um die Alignment-Reihenfole zu ändern; Sie können eine Untermenge an Sequenzen auswählen, die verglichen werden sollen; Sie können einen Teilbereich des Alignments auswählen, neu anordnen und wieder in das ursprüngliche Alignment einfügen.

Es kann eine Qualitätsanlayse des Alignments durchgeführt werden. Außerdem können Segmente mit geringem Score oder ungewöhnlichen Resten hervorgehoben werden.

Das Kommandozeilenwerkzeug DIALIGN2 führt ein multiples Alignment von Protein- oder DNA-Sequenzen aus. Es erstellt Alignments aus gap-freien Paaren von ähnlichen Sequenzsegmenten. Dieses Bewertungsverfahren ist der grundlegende Unterschied zwischen DIALIGN und anderen globalen oder lokalen Methoden für Sequenzalignments. Beachten Sie, dass DIALIGN bei Gaps das Ergebnis nicht schlechter bewertet.

DIALIGN-TX ist ein Kommandozeilenwerkzeug, um mehrere Protein- oder DNA-Sequenzen aneinander auszurichten (»zu alignen«). Es handelt sich um eine vollständige Reimplementation des segmentbasierten Ansatzes, einschließlich einiger neuer Verbesserungen und Heuristiken und anderer Verbesserungen, die im Vergleich mit DIALIGN 2.2 oder DIALIGN-T deutlich die Qualität der ermittelten Alignments erhöht. Für paarweise Alignments nutzt DIALIGN-TX einen Algorithmus zur Verkettung von Fragmenten, der Ketten niedrig bewerteter lokaler Alignments den isolierten höher bewerteten Fragmenten vorzieht. Für multiple Alignments nutzt DIALIGN-TX eine verbesserte, erfolgshungrige Prozedur, die nicht auf falsche lokale Sequenzähnlichkeiten hereinfällt.

Mit Exonerate können Sie Sequenzen ab- und vergleichen. Das Programm bietet Ihnen viele Alignment-Modelle, welche entweder vollständig dynamische Programmierung oder eine Reihe von heuristischen Methoden verwenden. Ein Großteil der Funktionalität der »Wise dynamic programming suite« wurde zur Erhöhung der Effizienz in C neu geschrieben. Exonerate ist eine wesentliche Komponente bei der Erstellung der »Ensembl Genome«-Datenbanken, die Ähnlichkeitsmaße für RNA- und DNA-Sequenzen bestimmt und so allgemein »splice variants« und Codesequenzen bestimmt.

Ein »In-silico PCR«-System zur Simulation von Experimenten (Siehe auch das Handbuch von »ipcress«) wird zusammen mit »exonerate« verteilt.

Dieses Paket beinhaltet auch eine Auswahl an Werkzeugen zur Erstellung einfacher, schneller Änderungen an »fasta«-Dateien mit über 2GB Dateigröße.

FastDNAml ist abgeleitet von Joseph Felsensteins DNAML Version 3.3 (Teil seines Pakets PHYLIP). Bevor Sie fastDNAml verwenden, sollten Sie die Dokumentation für DNAML heranziehen.

FastDNAml ist der Versuch, das gleiche Problem wie DNAML effektiver zu lösen, damit größere Bäume und/oder »bootstrap«-Replikate behandelt werden können. Bei großen Teilen von fastDNAml handelt es sich lediglich um eine Neuprogrammierung der in Pascal geschriebenen PHYLIP DNAML Version 3.3 in der Sprache C.

Beachten Sie, dass die Webseite dieses Programms nicht mehr verfügbar ist und dieses Programm daher wahrscheinlich nicht mehr aktualisiert wird.

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).

FigTree ist gedacht als grafischer Betrachter für phylogenetische Bäume und als ein Programm, das veröffentlichungsreife Abbildungen erstellt. Insbesondere ist es für die Anzeige zusammengefasster und annotierter Bäume geeignet, die von BEAST erstellt wurden.

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.

HMMER ist eine Implementierung der Profile-Hidden-Markov-Modelle für eine sensitive Suche in biologischen Sequenzdatenbanken mit multiplen Sequenzalignments als Anfragen.

Mit einem multiplen Sequenzalignment als Eingabe baut HMMER ein statistisches Modell, genannt »Hidden-Markov-Modell«. Mit diesem kann in Sequenzdatenbanken nach homologen Sequenzen gesucht werden. Dabei können gleichzeitig, der gesuchten Proteinfamilie zugehörige, Sequenzen alignt werden.

IQ-TREE is a very efficient maximum likelihood phylogenetic software with following key features among others:

• A novel fast and effective stochastic algorithm to estimate maximum likelihood trees. IQ-TREE outperforms both RAxML and PhyML in terms of likelihood while requiring similar amount of computing time (see Nguyen et al., 2015)
• An ultrafast bootstrap approximation to assess branch supports (see Minh et al., 2013).
• A wide range of substitution models for binary, DNA, protein, codon, and morphological alignments.
• Ultrafast model selection for all data types, 10 to 100 times faster than jModelTest and ProtTest.
• Finding best partition scheme like PartitionFinder.
• Partitioned models with mixed data types for phylogenomic (multi- gene) alignments, allowing for separate, proportional, or joint branch lengths among genes.
• Supporting the phylogenetic likelihod library (PLL) (see Flouri et al., 2014)

jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision theory method (DT). It also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged tree topologies. jModelTest 2 includes High Performance Computing (HPC) capabilities and additional features like new strategies for tree optimization, model- averaged phylogenetic trees (both topology and branch length), heuristic filtering and automatic logging of user activity.

Das Befehlszeilenwerkzeug Kalign gleicht mehrere biologische Sequenzen ab. Für die Erhöhung von Präzision und Geschwindigkeit nutzt es den Muth-Manber-Algorithmus, der in großen Datenmengen sich wiederholende Muster ermittelt. Das Programm verwendet einen globalen, fortschreitenden Alignment-Ansatz, ergänzt durch den Einsatz eines annähernden Musterabgleich-Algorithmus zur Berechnung von Sequenzabständen und durch die Einbeziehung lokaler Übereinstimmungen in ein ansonsten globales Alignment.

Die Bayessche Inferenz der Phylogenie basiert auf einer Quantität - A-posteriori-Wahrscheinlichkeitsverteilung von Bäumen genannt - die die Wahrscheinlichkeit eines Baumes bedingt durch die Beobachtungen ist. Die Bedingung entsteht durch Verwendung des Bayestheorems. Die A-posteriori-Wahrscheinlichkeitsverteilung von Bäumen kann unmöglich analytisch berechnet werden. Stattdessen verwendet MrBayes eine Simulation, das Markov-Chain-Monte-Carlo-Verfahren (kurz MCMC), um die A-posteriori-Wahrscheinlichkeiten der Bäume zu schätzen.

MUSCLE is a multiple alignment program for protein sequences. MUSCLE stands for multiple sequence comparison by log-expectation. In the authors tests, MUSCLE achieved the highest scores of all tested programs on several alignment accuracy benchmarks, and is also one of the fastest programs out there.

Muscle v5 is a major re-write of MUSCLE based on new algorithms.

Users should be aware that command line arguments compared to version 3.x of MUSCLE have changed!

Highest accuracy, scalable to thousands of sequences

Compared to previous versions, Muscle v5 is much more accurate, is often faster, and scales to much larger datasets. At the time of writing (late 2021), Muscle v5 has the highest scores on multiple alignment benchmarks including Balibase, Bralibase, Prefab and Balifam. It can align tens of thousands of sequences with high accuracy on a low-cost commodity computer (say, an 8-core Intel CPU with 32 Gb RAM). On large datasets, Muscle v5 is 20-30% more accurate than MAFFT and Clustal-Omega.

Alignment ensembles

Muscle v5 can generate ensembles of high-accuracy alternative alignments. All replicates have equal average accuracy on benchmark test, including the MSA made with default parameters. By comparing results of downstream analysis (trees, structure prediction...) on different replicates, you can assess the effects of alignment errors on your study.

MUSCLE is a multiple alignment program for protein sequences. MUSCLE stands for multiple sequence comparison by log-expectation. In the authors tests, MUSCLE achieved the highest scores of all tested programs on several alignment accuracy benchmarks, and is also one of the fastest programs out there.

This is version 3 of the muscle program. It is a different program than muscle version 5 which is packaged as muscle in Debian.

Mustang ist ein Algorithmus, um mehrere Protein-Strukturen miteinander abzugleichen. Aus einem Satz von PDB-Dateien (Protein Data Bank, PDB) bestimmt das Programm unter Ausnutzung der räumlichen Informationen in den Calpha-Atomen die einander zuzuordnenden Aminosäuren. Dies ist für verschiedene Bereiche des Proteins auch unterschiedlich gut möglich. Anschließend werden die Proteine paarweise miteinander verglichen, und so in mehreren Durchgängen mit einer Heuristik das Ergebnis zunehmend verfeinert. Schließlich gibt Mustang die Zuordnung der Protein-Sequenzen (das Alignment) und auch die entsprechende räumliche Überlagerung von Strukturen aus.

NJplot kann alle Dendrogramme zeichnen, die im Newick-Format notiert sind. Dieses Format ist das Standardformat für phylogenetische Bäume (und wird z.B. vom Phylip-Paket verwendet). NJplot ist besonders praktisch, um mit den Baumerstellungsmethoden parsimony, distance oder maximum-likelihood erzeugte ungewurzelte Bäume in gewurzelte Bäume zu überführen.

The PHYLogeny Inference Package is a package of programs for inferring phylogenies (evolutionary trees) from sequences. Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites, distance matrices, and 0/1 discrete characters.

PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test).

PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the “comfort zone” for PhyML generally lies around 3 to 500 sequences less than 2,000 character long.

This package also includes PhyTime.

POA is Partial Order Alignment, a fast program for multiple sequence alignment (MSA) in bioinformatics. Its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment. Partial order alignment is an approach to MSA, which can be combined with existing methods such as progressive alignment. POA optimally aligns a pair of MSAs and which therefore can be applied directly to progressive alignment methods such as CLUSTAL. For large alignments, Progressive POA is 10-30 times faster than CLUSTALW.

Populations is a population genetic software. It computes genetic distances between populations or individuals. It builds phylogenetic trees (NJ or UPGMA) with bootstrap values.

Pplacer places reads on a phylogenetic tree. guppy (Grand Unified Phylogenetic Placement Yanalyzer) yanalyzes them. rppr is a helpful tool for working with reference packages.

Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.

ProAlign performs probabilistic sequence alignments using hidden Markov models (HMM). It includes a graphical interface (GUI) allowing to (i) perform alignments of nucleotide or amino-acid sequences, (ii) view the quality of solutions, (iii) filter the unreliable alignment regions and (iv) export alignments to other software.

ProAlign uses a progressive method, such that multiple alignment is created stepwise by performing pairwise alignments in the nodes of a guide tree. Sequences are described with vectors of character probabilities, and each pairwise alignment reconstructs the ancestral (parent) sequence by computing the probabilities of different characters according to an evolutionary model.

Probalign uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments. It performs statistically significantly better than the leading alignment programs Probcons v1.1, MAFFT v5.851, and MUSCLE v3.6 on BAliBASE 3.0, HOMSTRAD, and OXBENCH benchmarks. Probalign improvements are largest on datasets containing N/C terminal extensions and on datasets with long and heterogeneous length sequences. On heteregeneous length datasets containing repeats Probalign alignment accuracy is 10% and 15% higher than the other three methods when standard deviation of length is at least 300 and 400.

Tool for generating multiple alignments of protein sequences. Using a combination of probabilistic modeling and consistency-based alignment techniques, PROBCONS has achieved the highest accuracies of all alignment methods to date. On the BAliBASE benchmark alignment database, alignments produced by PROBCONS show statistically significant improvement over current programs, containing an average of 7% more correctly aligned columns than those of T-Coffee, 11% more correctly aligned columns than those of CLUSTAL W, and 14% more correctly aligned columns than those of DIALIGN.

ProDA ist ein System zur automatischen Erkennung und Anordnung von homologen Regionen in Proteinsammlungen mit beliebigen Domain-Architekturen. Bei gegebenem Eingangssatz von nicht-angeordneten Sequenzen identifiziert ProDA eine homologe Region, die in einer oder mehrere Sequenzen auftaucht und liefert eine Sammlung von lokalen multiplen Anordnungen für diese Regionen zurück.

PROTTEST (ModelTest's relative) is a program for selecting the model of protein evolution that best fits a given set of sequences (alignment). This java program is based on the Phyml program (for maximum likelihood calculations and optimization of parameters) and uses the PAL library as well. Models included are empirical substitution matrices (such as WAG, LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam, MtArt, HIVb, and HIVw) that indicate relative rates of amino acid replacement, and specific improvements (+I:invariable sites, +G: rate heterogeneity among sites, +F: observed amino acid frequencies) to account for the evolutionary constraints impossed by conservation of protein structure and function. ProtTest uses the Akaike Information Criterion (AIC) and other statistics (AICc and BIC) to find which of the candidate models best fits the data at hand.

QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing phylogenies from huge alignments in time less than the age of the universe.

QuickTree accepts both distance matrix and multiple-sequence-aligment inputs. The former should be in PHYLIP format. The latter should be in Stockholm format, which is the native alignment format for the Pfam database. Alignments in various formats can be converted to Stockholm format with the sreformat program, which is part of the HMMer package (hmmer.org).

The tress are written to stdout, in the Newick/New-Hampshire format use by PHYLIP and many other programs

SeaView is a viewer and editor of multiple sequence alignments, i.e. DNA or protein sequences are positioned each in their own separate line, such that the nucleotide/amino acid at a particular position (column) is presumed to have the same biochemical property.

SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees. Alignments can be manually edited. It drives the programs Muscle or Clustal Omega for multiple sequence alignment, and also allows one to use any external alignment algorithm able to read and write FASTA-formatted files. It computes phylogenetic trees by parsimony using PHYLIP's dnapars/protpars algorithm, by distance with NJ or BioNJ algorithms on a variety of evolutionary distances, or by maximum likelihood using the program PhyML 3.0.

SeaView draws phylogenetic trees on screen or PostScript files, and allows one to download sequences from EMBL/GenBank/UniProt using the Internet.

Sigma (»Simple greedy multiple alignment«) ist ein Alignment-Programm. Der Algorithmus und das Scoring-Schema sind speziell für nicht-kodierende DNA-Sequenzen entworfen.

Das Programm verwendet die Strategie des Suchens der bestmöglichen lückenlosen lokalen Alignments. Dies passiert bei jedem Schritt indem ein bestmögliches Alignment passend zu existierenden Alignments ermittelt wird. Sigma bewertet die Signifikanz der Alignments basierend auf den Längen der alignierten Fragmente und eines Hintergrundmodells. Diese können über eine Hilfsdatei intergenischer DNA zur Verfügung gestellt oder geschätzt werden.

SPREAD is a user-friendly application to analyze and visualize phylogeographic reconstructions resulting from Bayesian inference of spatio-temporal diffusion.

There is a tutorial for SPREAD online at http://www.kuleuven.be/aidslab/phylogeography/tutorial/spread_tutorial.html

Originally this program is named "spread". However, there is just such a package inside Debian and thus a 'phy' for phylogeny was prepended.

T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures.

T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model. It can also estimate the level of consistency of each position within the new alignment with the rest of the alignments. See the pre-print for more information

T-Coffee has a special called M-Coffee that makes it possible to combine the output of many multiple sequence alignment packages. In its published version, it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA and T-Coffee. A special version has been made for Debian, DM-Coffee, that uses only free software by replacing Clustal W by Kalign. Using the 8 Methods of M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite methods if you prefer.

TM-align is a computer algorithm for protein structure alignment using dynamic programming. The scoring is performed by the TM-score rotation matrix. This is similar to the RMSD in that unaligned portions of the structure influence the scoring less than the more structurally conserved regions.

TREE-PUZZLE (früher PUZZLE) ist ein interaktives Konsolenprogramm, das einen schnellen Suchalgorithmus über einen Baum, sogenanntes »Quartet Puzzling«, implementiert. Es erlaubt die Analyse großer Datenmengen und trifft automatisch Entscheidungen über die Anordnung der jeweiligen Verzweigungen. Weiterhin berechnet TREE-PUZZLE mittels der paarweisen Maximum-Likelihood-Methode Abstände und Längen von Verzweigungen für vom Benutzer definierte Bäume. Die Längen der Verzweigungen können auch unter der »Clock-Assumption« berechnet werden. Außerdem bietet TREE-PUZZLE eine neue Methode, das »Likelihood Mapping«, um die Anordnung einer hypothetischen internen Verzweigung zu untersuchen, ohne den gesamten Baum zu berechnen und um den phylogenetischen Zusammenhang eines Sequenzalignments anzuzeigen.

Dies ist eine parallelisierte Version von tree-puzzle.

TREE-PUZZLE (früher PUZZLE) ist ein interaktives Konsolenprogramm, das einen schnellen Suchalgorithmus über einen Baum, sogenanntes »Quartet Puzzling«, implementiert. Es erlaubt die Analyse großer Datenmengen und trifft automatisch Entscheidungen über die Anordnung der jeweiligen Verzweigungen. Weiterhin berechnet TREE-PUZZLE mittels der paarweisen Maximum-Likelihood-Methode Abstände und Längen von Verzweigungen für vom Benutzer definierte Bäume. Die Längen der Verzweigungen können auch unter der »Clock-Assumption« berechnet werden. Außerdem bietet TREE-PUZZLE eine neue Methode, das »Likelihood Mapping«, um die Anordnung einer hypothetischen internen Verzweigung zu untersuchen, ohne den gesamten Baum zu berechnen und um den phylogenetischen Zusammenhang eines Sequenzalignments anzuzeigen.

TreeView creates a matrix-like display of expression data, known as Eisen clustering. The original implementation was a Windows program named TreeView by Michael Eisen. This TreeView package, sometimes also referred to as jTreeView, was rewritten in Java under a free license.

Java TreeView is an extensible viewer for microarray data in PCL or CDT format.

TreeViewX ist ein für mehrere Plattformen verfügbares Programm zur Darstellung phylogenetischer Bäume. Es kann Bäume in den Formaten NEXUS und Newick lesen und darstellen (so wie die, die von PAUP*, ClustalX, TREE-PUZZLE und anderen Programmen ausgegeben werden). Es ermöglicht das Anordnen der Zweige der Bäume und den Export der Bäume in das SVG-Format.

VeryFastTree is a highly efficient implementation inspired by the FastTree-2 tool, designed to expedite the inference of approximately-maximum-likelihood phylogenetic trees from nucleotide or protein sequence alignments. It is an optimized implementation designed to accelerate the estimation of phylogenies for large alignments. By leveraging parallelization and vectorization strategies, VeryFastTree significantly improves the performance and scalability of phylogenetic analysis, allowing it to construct phylogenetic trees in a fraction of the time previously required.

Maintaining the integrity of FastTree-2, VeryFastTree retains the same phases, methods, and heuristics used for estimating phylogenetic trees. This ensures that the topological accuracy of the trees produced by VeryFastTree remains equivalent to that of FastTree-2. Moreover, unlike the parallel version of FastTree-2, VeryFastTree guarantees deterministic results, eliminating any potential variations in the output.

To facilitate a seamless transition for users, VeryFastTree adopts the exact same command line arguments as FastTree-2. This means that by simply substituting FastTree-2 with VeryFastTree, and using the same set of options, users can significantly enhance the overall performance of their phylogenetic analyses.

TreeTime provides routines for ancestral sequence reconstruction and the maximum likelihoo inference of molecular-clock phylogenies, i.e., a tree where all branches are scaled such that the locations of terminal nodes correspond to their sampling times and internal nodes are placed at the most likely time of divergence.

TreeTime aims at striking a compromise between sophisticated probabilistic models of evolution and fast heuristics. It implements GTR models of ancestral inference and branch length optimization, but takes the tree topology as given. To optimize the likelihood of time-scaled phylogenies, treetime uses an iterative approach that first infers ancestral sequences given the branch length of the tree, then optimizes the positions of unconstraine d nodes on the time axis, and then repeats this cycle. The only topology optimization are (optional) resolution of polytomies in a way that is most (approximately) consistent with the sampling time constraints on the tree. The package is designed to be used as a stand-alone tool or as a library used in larger phylogenetic analysis workflows.

Features

• ancestral sequence reconstruction (marginal and joint maximum likelihood)
• molecular clock tree inference (marginal and joint maximum likelihood)
• inference of GTR models
• rerooting to obtain best root-to-tip regression
• auto-correlated relaxed molecular clock (with normal prior)

This package provides the Python 3 module.

Archaeopteryx is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees. It can be used both as applet (ArchaeopteryxA and ArchaeopteryxE) and as a standalone application.

Patristic overcomes some logistic barriers to analysing signals in sequences. In additional to calculating patristic distances, it provides plots for any combination of matrices, calculates commonly used statistics, allows data such as isolation dates to be entered and reorders matrices with matching species or gene labels. It will be used to analyse rates of mutation and substitutional saturation and the evolution of viruses.

Phylo_win is a graphical colour interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony and maximum likelihood methods and bootstrap with any of them. Many distances can be used including Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy (1995), LogDet for nucleotidic sequences, Poisson correction for protein sequences, Ka and Ks for codon sequences. Species and sites to include in the analysis are selected by mouse. Reconstructed trees can be drawn, edited, printed, stored and evaluated according to numerous criteria.

This program uses sources files from the Phylip program, which forbids its use for profit. Therfore, Phylo_win will unfortunately have to be distributed in contrib or non-free.

gBioSeq is in an early stage of development, but it is already running. The goal is to provide an easy to use software to edit DNA sequences under Linux, Windows, MacOsX, using GTK C# (Mono).

A concise viewer/editor for phylogenetic trees in the Newick format. The core functions are written in JavaScript, using the canvas tag proposed by HTML 5. No server side support is needed for rendering the picture and therefore you can grab this page together with knhx.js and canvastext.js to locally view your trees in a supported web browser.

The source can be downloaded at http://www.sanger.ac.uk/Users/lh3/download/jstreeview.zip

PhpPhylotree is a web application that is able to draw phylogenetic trees. It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.

TreeTime is controlled by input files in nexus format and does bayesian sampling of phylogenetic trees from these data.