Debian Med Phylogeny packages

ALTree został zaprojektowany do wykrywania związku oraz wyszukiwania miejsc podatnych na zakażenie przy użyciu drzew filogenetycznych haplotypu: po pierwsze, umożliwia wykrycie związku pomiędzy genem kandydującym a chorobą, i po drugie, pozwala na postawienie hipotezy na temat podatności loci.

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.

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.

This package offers a GUI interface for the Clustal multiple sequence alignment program. It provides an integrated environment for performing multiple sequence- and profile-alignments to analyse the results. The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated to highlight conserved features in the alignment. For professional presentations, one should use the texshade LaTeX package or boxshade.

The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment. You can cut-and-paste sequences to change the order of the alignment; you can select a subset of sequences to be aligned; you can select a sub-range of the alignment to be realigned and inserted back into the original alignment.

An alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted.

DIALIGN2 to narzędzie używane w wierszu poleceń do wykonywania wielu dopasowań sekwencji białek lub DNA. Tworzy ono dopasowania z pozbawionych przerw par podobnych segmentów sekwencji. Ten schemat punktacji dla dopasowań stanowi podstawową różnicę pomiędzy DIALIGN a innymi globalnymi lub lokalnymi metodami dopasowania sekwencji. Należy pamiętać, że DIALIGN nie ocenia wyniku gorzej w przypadku przerw.

DIALIGN-TX is a command line tool to perform multiple alignment of protein or DNA sequences. It is a complete reimplementation of the segment-base approach including several new improvements and heuristics that significantly enhance the quality of the output alignments compared to DIALIGN 2.2 and DIALIGN-T. For pairwise alignment, DIALIGN-TX uses a fragment-chaining algorithm that favours chains of low-scoring local alignments over isolated high-scoring fragments. For multiple alignment, DIALIGN-TX uses an improved greedy procedure that is less sensitive to spurious local sequence similarities.

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

Aplikacja fastDNAml wywodzi się z programu DNAML w wersji 3.3 Josepha Felsensteina (część jego pakietu PHYLIP). Użytkownicy powinni zapoznać się z dokumentacją DNAML przed użyciem tego programu.

Program próbuje rozwiązywać te same problemy co DNAML, ale robi to szybciej przy mniejszym obciążeniu pamięci, co umożliwia łatwe zarządzanie większymi drzewami i/lub ponownymi próbkami danych wejściowych. Znaczna część fastDNAml jest jedynie przekodowanym z języka Pascal do C programem DNAML 3.3 z pakietu PHYLIP (PHYLogeny Inference Package).

Należy pamiętać, że strona główna programu nie jest już dostępna, więc prawdopodobnie nie będzie on dalej aktualizowany.

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 został zaprojektowany jako graficzna przeglądarka drzew filogenetycznych oraz jako program do tworzenia figur gotowych do publikacji. W szczególności przeznaczony jest do wyświetlania podsumowanych i opatrzonych adnotacjami drzew stworzonych przez BEAST.

Pakiet ten zawiera programy GMAP i GSNAP oraz narzędzia do zarządzania bazami danych genomów w formacie GMAP/GSNAP. GMAP (Genomic Mapping and Alignment Program) to narzędzie służące do dopasowywania sekwencji EST, mRNA i cDNA. GSNAP (Genomic Short-read Nucleotide Alignment Program) to narzędzie do dopasowywania odczytów transkryptomu z pojedynczym i sparowanym końcem. Obydwa narzędzia mogą korzystać z bazy danych:

• znanych miejsc splotów i zidentyfikować nowe tego typu miejsca.
• znanych polimorfizmów pojedynczych nukleotydów (SNP). GSNAP może wyrównać DNA poddanemu działaniu wodorosiarczynu.

HMMER is an implementation of profile hidden Markov model methods for sensitive searches of biological sequence databases using multiple sequence alignments as queries.

Given a multiple sequence alignment as input, HMMER builds a statistical model called a "hidden Markov model" which can then be used as a query into a sequence database to find (and/or align) additional homologues of the sequence family.

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.

Kalign jest narzędziem wiersza poleceń do przeprowadzenia wielokrotnego dopasowywania sekwencji biologicznych. Wykorzystuje algorytm dopasowywania ciągów Mutha-Manbera do poprawiania zarówno dokładności, jak i szybkości wyrównywania. Program wykorzystuje globalne, progresywne podejście do dopasowywania, wzbogacone o zastosowanie przybliżonego algorytmu dopasowywania ciągów do obliczania odległości sekwencji oraz poprzez włączenie lokalnych dopasowań do globalnego wyrównywania.

Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.

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 to algorytm dopasowywania wielu struktur białkowych. Program wykorzystuje informacje przestrzenne zawarte w atomach Calpha z zestawu plików PDB w celu uzyskania dopasowania sekwencji. W oparciu o progresywną heurystykę dopasowywania parami algorytm przechodzi przez szereg przejść udoskonalających. Mustang raportuje dopasowanie wielu sekwencji i odpowiednią superpozycję struktur.

NJplot jest w stanie narysować dowolny dendrogram wyrażony w standardowym formacie drzewa filogenetycznego Newick (np. formacie używanym przez pakiet Phylip). NJplot jest szczególnie wygodny do ukorzeniania nieukorzenionych drzew uzyskanych metodami oszczędzania, odległości lub maksymalnego prawdopodobieństwa.

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 to oprogramowanie do genetyki populacji. Oblicza odległości genetyczne między populacjami lub osobnikami. Buduje drzewa filogenetyczne (NJ lub UPGMA) z wartościami bootstrap.

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 to system do automatycznego wykrywania i wyrównywania homologicznych regionów w zestawach białek o dowolnej domenowej architekturze. Po pobraniu wejściowego zestawu niewyrównanych sekwencji, ProDA identyfikuje wszystkie homologiczne regiony, pojawiające się w jednej lub większej liczbie sekwencji, i zwraca zbiór lokalnych wielokrotnych wyrównań dla tych regionów.

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”) is an alignment program. It's algorithm and scoring scheme are designed specifically for non-coding DNA sequence.

It uses a strategy of seeking the best possible gapless local alignments. This happens at each step making the best possible alignment consistent with existing alignments. It scores the significance of the alignment based on the lengths of the aligned fragments and a background model. These may be supplied or estimated from an auxiliary file of intergenic DNA.

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 jest pakietem do wielosekwencyjnego wyrównania. Generuje wiele sekwencji wyrównania z zestawu sekwencji białka lub DNA.

T-Coffee pozwala na kombinację zbiorów złożonych z wielu par, globalne lub lokalne wyrównania w pojedynczym modelu. Umożliwia także oszacowywanie poziomu spójności każdej pozycji w nowym wyrównaniu z resztą wyrównań. Aby uzyskać więcej informacji, należy zapoznać się z przedrukami dokumentacji.

T-Coffee zawiera specjalny dodatek o nazwie M-Coffee, który umożliwia połączenie danych wyjściowych z wielu pakietów wielosekwencyjnych wyrównań. W opublikowanej wersji używa: MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA i T-Coffee. Specjalna wersja stworzona do Debiana, DM-Coffee, korzysta tylko z wolnego oprogramowania, zastępując Clustal W przez Kalign. Korzystanie z tych 8 metod z M-Coffee może być nieco trudne. Można również używać ulubionego podzbioru metod.

TM-align to algorytm komputerowy, służący do dopasowywania struktury białek przy użyciu programowania dynamicznego. Punktacja przeprowadzana jest za pomocą rotacji macierzy TM-score. Przypomina to RMSD, ponieważ niewyrównane części struktury wpływają na punktację w mniejszym stopniu niż regiony bardziej konserwatywne strukturalnie.

TREE-PUZZLE (the new name for PUZZLE) is an interactive console program that implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can also be calculated under the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment.

This is the parallelized version of tree-puzzle.

TREE-PUZZLE (nowa nazwa dla programu PUZZLE) to interaktywny program konsolowy, który implementuje algorytm (quartet puzzling) do szybkiego przeszukiwania drzew, umożliwiający analizę dużych zbiorów danych i automatycznie przypisujący estymacje wsparcia do każdej wewnętrznej gałęzi. TREE-PUZZLE oblicza również maksymalne prawdopodobieństwo oddalenia par oraz długości gałęzi dla drzew określonych przez użytkownika. Długość gałęzi można również obliczyć, przyjmując założenia zegara. Ponadto TREE-PUZZLE oferuje nowatorską metodę mapowania prawdopodobieństwa, która pozwala na zbadanie wsparcia hipotetycznej gałęzi wewnętrznej bez konieczności obliczania całego drzewa oraz na wizualizację zawartości filogenetycznej dopasowania sekwencji.

TreeView tworzy macierzową prezentację danych wyrażeń, znaną jako grupowanie Eisena. Oryginalną implementacją był program dla Windows * nazwie TreeView autorstwa Michaela Eisena. Ten pakiet TreeView, czasami nazywany także jTreeView, został przepisany w Javie na wolnej licencji.

Java TreeView to rozszerzalna przeglądarka danych mikromacierzy w formacie PCL lub CDT.

TreeView X to wieloplatformowy program o otwartym kodzie źródłowym do wyświetlania drzew filogenetycznych. Może odczytywać i wyświetlać pliki drzew w formatach NEXUS i Newick (jak te generowane przez programy PAUP*, ClustalX, TREE-PUZZLE i inne). Umożliwia porządkowanie gałęzi drzew i eksportowanie tych drzew w formacie SVG.

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.