Changes

Waiting list

Other lists

Old programs

Not listed

???

Here are 376 phylogeny packages and 50 free servers, all that I know about. It is an attempt to be completely comprehensive. I have not made any attempt to exclude programs that do not meet some standard of quality or importance. Updates to these pages are made roughly weekly. Here is a "waiting list" of new programs waiting to have their full entries constructed. Many of the programs in these pages are available on the web, and some of the older ones are also available from ftp server machines.

The programs listed below include both free and non-free ones; in some cases I do not know whether a program is free. I have listed as free those that I knew were free; for the others you have to ask their distributor. Usually when I say that a program is downloadable from a web site, this means that it is available free.

Email addresses in these pages have had the @ symbol replaced by (at) and also surrounded by invisible confusing tags and blank characters in hopes of foiling spambots that harvest email addresses.

If you discover any inaccuracies, or feel that I have left any important programs or facts out, or if links do not work properly, please e-mail me at: (joe (at) gs.washington.edu). You can also use the submission form here to submit new entries.

... by methods available

... by computer systems on which they work

... cross-referenced by method and by computer system.

... by ones which analyze particular kinds of data.

... to show the most recent listings

... to show ones most recently changed

Phylogeny programs formerly listed here but no longer distributed

Which kinds of programs are and are not listed

Other lists of phylogeny software

New programs waiting to be added

General-purpose packages

• PHYLIP
• PAUP*
• MEGA
• Phylo_win
• ARB
• DAMBE
• PAL
• Bionumerics
• Mesquite
• PaupUp
• BIRCH
• Bosque

Parsimony programs

PAUP* Hennig86 MEGA RA Nona PHYLIP CAFCA Phylo_win sog gmaes LVB GeneTree TAAR ARB DAMBE MALIGN POY Gambit TNT GelCompar II Bionumerics Network TCS GAPars CRANN

PAUPRat Mesquite PAST FootPrinter BPAnalysis Simplot Parsimov NimbleTree PaupUp Notung galaxie BIRCH IDEA PSODA PRAP SeqState Bosque PhyloNet

Distance matrix methods

PHYLIP PAUP* MEGA MacT ODEN TREECON DISPAN RESTSITE NTSYSpc METREE TreeTree GDA Hadtree, Prepare and Trees GCG Wisconsin Package SeqPup PHYLTEST Lintre WET Phylo_win POPTREE Gambit gmaes DENDRON Fingerprinting II Informatix Software BIONJ

TFPGA MVSP ARB Darwin T-REX sendbs nneighbor DAMBE weighbor DNASIS MINSPNET PAL Arlequin vCEBL HY-PHY Vanilla GelCompar II Bionumerics qclust TCS Populations Winboot SYN-TAX PTP SplitsTree

FastME APE MacVector Discovery Studio Gene QuickTree Simplot ProfDist START STC NimbleTree CBCAnalyzer PaupUp galaxie Geneious BIRCH SEMPHY FASTML Rate4Site SWORDS IDEA FAMD Bosque GAME Bioinformatics_Toolbox

Computation of distances

PHYLIP PAUP* RAPDistance MULTICOMP Microsat DIPLOMO OSA DISPAN RESTSITE NTSYSpc TREE-PUZZLE Hadtree, Prepare and Trees GCG Wisconsin Package AMP GCUA DERANGE2 POPGENE TFPGA REAP MVSP RSTCALC Genetix DISTANCE Darwin sendbs

K2WuLi GeneStrut Arlequin DAMBE DnaSP PAML puzzleboot PAL Vanilla GelCompar II Bionumerics qclust Populations Winboot FSTAT SYN-TAX Phylo_win Phyltools MSA APE YCDMA NSA T-REX LDDist DIVAGE

Genepop START Swaap Swaap PH GeneContent SPAGeDi CBCAnalyzer PaupUp SEMPHY SWORDS rRNA phylogeny FAMD GAME Bioinformatics_Toolbox GenoDive

Maximum likelihood and Bayesian methods

PHYLIP PAUP* fastDNAml MOLPHY PAML Spectrum SplitsTree PLATO TREE-PUZZLE Hadtree, Prepare and Trees SeqPup Phylo_win PASSML ARB Darwin BAMBE DAMBE Modeltest TreeCons VeryfastDNAml PAL dnarates TrExMl HY-PHY Vanilla

DT-ModSel Bionumerics fastDNAmlRev RevDNArates rate-evolution MrBayes CONSEL PAUPRat EDIBLE Mesquite PTP Treefinder MetaPIGA RAxML PHASE PHYML BEAST r8s-bootstrap MrBayes tree scanners MrMTgui MrModeltest BootPHYML p4 Porn* SIMMAP

Spectronet Rhino IM ProtTest ModelGenerator Simplot MDIV MrAIC Modelfit IQPNNI PARAT ALIFRITZ PhyNav DPRML MultiPhyl NimbleTree PaupUp SSA BAli-Phy CoMET BIRCH Mac5 BayesPhylogenies Kakusan2 GARLI

PHYSIG MrBayesPlugin SEMPHY FASTML Rate4Site aLRT McRate PhyloBayes BEST EREM IDEA PROCOV DART PhyloCoCo AMBIORE PRAP SeqState Leaphy NHML SLR rRNA phylogeny Bosque Concaterpillar PHYLLAB NEPAL

Quartets methods

• TREE-PUZZLE
• SplitsTree
• PHYLTEST
• GEOMETRY
• PICA
• Darwin
• PhyloQuart
• Willson quartets programs
• Gambit
• IQPNNI
• STC
• Quartet Suite
• LEVEL2
• Bosque

Artificial-intelligence and genetic algorithms methods

• PTP
• GAPars
• MetaPIGA
• GARLI

Invariants (or Evolutionary Parsimony) methods

• PHYLIP
• PAUP*
• PaupUp
• BIRCH

Interactive tree manipulation

MacClade PHYLIP PDAP TreeTool ARB WINCLADA TreeEdit TreeExplorer TreeThief RadCon Mavric T-REX EDIBLE Mesquite Treefinder TreeView TreeJuxtaposer TreeMe ArboDraw Notung TreeDyn TreeMaker BIRCH SimpleClade TreeIllustrator

Dendroscope Forest Phylocom TreeToy Bioinformatics_Toolbox

Looking for hybridization or recombination events

PLATO reticulate RecPars TOPALi partimatrix LARD Network TCS SiScan T-REX PPH Spectronet PIST IM Simplot START Likewind DualBrothers cBrother TreeMos EEEP HGT PhyloNet EvolSimulator

Concaterpillar Codeml3X

Bootstrapping and other measures of support

PHYLIP PAUP* Random Cladistics AutoDecay TreeRot DNA Stacks OSA DISPAN TreeTree PHYLTEST Lintre sog POPTREE MEGA PICA ModelTest TAXEQ3 TreeCons BAMBE DAMBE puzzleboot CodonBootstrap Gambit TrExMl PAL

PHYCON MrBayes CONSEL Populations LVB EDIBLE Winboot Mesquite Phylo_win PAST Treefinder RAxML Phyltools PHASE PHYML BEAST r8s-bootstrap MrBayes tree scanners T-REX MrMTgui MrModeltest BootPHYML Porn* Discovery Studio Gene ProtTest

ModelGenerator Simplot MCS Permute! ELW MultiPhyl GHOSTS PaupUp Geneious BIRCH BayesPhylogenies scaleboot aLRT PhyloBayes SWORDS CTree PRAP FAMD bootscore PhyloNet PHYLLAB

Compatibility analysis

• COMPROB
• PHYLIP
• PICA
• reticulate
• partimatrix
• CLINCH
• PPH
• Spectronet
• BIRCH

Consensus trees, subtrees, supertrees, and distances between trees

COMPONENT TREEMAP NTSYSpc PHYLIP PAUP* REDCON TAXEQ3 TreeCons MEGA RadCon Mesquite PAST Treefinder Robinson and Foulds distance Clann PhyNav SuperTree Supertree scripts PaupUp Supertree BIRCH HeuristicMRF2 TopD/fMts Quartet Suite Rainbow

PhySIC EEEP PhyloSort FAMD bootscore PhyloNet

Tree-based sequence alignment

• TreeAlign
• ClustalW
• MALIGN
• GeneDoc
• GCG Wisconsin Package
• TAAR
• Ctree
• DAMBE
• POY
• ALIGN
• DNASIS
• FootPrinter
• ALIFRITZ
• T-Coffee
• ArboDraw
• BAli-Phy
• galaxie
• Geneious
• BIRCH
• MAFFT
• SATCHMO
• DART
• MUSCLE
• Bosque

Gene duplication and genomic analysis

• DERANGE2
• FORESTER
• Mgenome
• BPAnalysis
• GeneContent
• Notung
• TopD/fMts
• DTscore
• DART
• gtp
• EvolSimulator
• DTdraw

Biogeographic analysis and host-parasite comparison

• COMPONENT
• TREEMAP
• DIVA
• TreeFitter
• GEODIS
• MDIV
• Tarzan
• ParaFit
• Phylocom
• AxParafit

Comparative method analysis

PHYLIP CAIC COMPARE CMAP CoSta PDAP ACAP ANCML RIND MacroCAIC Phylogenetic Independence MacClade Mesquite APE Jevtrace SIMMAP PHYLOGR TreeSAAP Permute! Parsimov DIVERGE IDC OUCH BIRCH BayesTraits

PHYSIG Cactus-Pie Phylocom pcca

Simulation of trees or data

COMPONENT Bi-De Seq-Gen Treevolve and PTreevolve PSeq-Gen COMPARE ROSE PAML ProSeq PAL Vanilla MacClade EDIBLE Mesquite Treefinder Network Hetero Phyl-O-Gen MESA SGRunner apTreeshape Simprot EREM indel-Seq-Gen DAWG

EvolveAGene3 EvolSimulator

Examination of shapes of trees

• MacroCAIC
• Genie
• PAL
• Vanilla
• RadCon
• BRANCHLENGTH
• APE
• Tracer
• SymmeTREE
• TreeScan
• MESA
• apTreeshape
• TreeStat
• CTree

Clocks, dating and stratigraphy

QDate Diversi K2WuLi Modeltest PAML TipDate RRTree vCEBL TreeEdit HY-PHY MEGA PAL rate-evolution BRANCHLENGTH r8s PAST Treefinder Network APE BEAST MrMTgui MrModeltest SymmeTREE Porn* Rhino

GHOSTS Cadence Multidivtime CodonRates BIRCH Brownie PATHd8 McRate PhyloBayes Cactus-Pie GRate NHML MULTIDIVTIME HELPER

Model Selection

• Modeltest
• MrMTgui
• MrModeltest
• Porn*
• ModelGenerator
• ProtTest
• MrAIC
• Modelfit
• DT-ModSel
• BayesTraits
• Kakusan2
• MAPPS
• DART
• Concaterpillar

Description or prediction of data from trees

• CONSERVE
• TreeDis
• EDIBLE
• RIND
• Jevtrace
• SIMMAP
• TreeSAAP
• DIVERGE
• MESA
• FASTML
• RPT

Tree plotting/drawing

PHYLIP PAUP* TreeTool TreeView NJplot DendroMaker Tree Draw Deck Phylodendron ARB unrooted DAMBE TREECON Mavric TreeExplorer TreeThief Bionumerics FORESTER MacClade MEGA Mesquite Phylogenetic Tree Drawing APE T-REX TreeJuxtaposer Spectronet

TreeSetViz TreeGraph ArboDraw PaupUp Notung TreeDyn DigTree Geneious BIRCH Paloverde MrEnt FigTree TreeIllustrator HyperTree GeoPhyloBuilder Dendroscope CTree RPT TreeToy TreeSnatcher DTdraw PHYLLAB Bioinformatics_Toolbox

Sequence management/job submission

• Random Cladistics
• GDE
• MUST 2000
• DNA Stacks
• SeqPup
• ARB
• DAMBE
• BioEdit
• Singapore PHYLIP web interface
• Bionumerics
• W2H
• Phyledit
• GeneStudio Pro
• Simplot
• DPRML
• NimbleTree
• galaxie
• Geneious
• BIRCH
• TOPALi
• MBEToolbox
• PISE
• Bosque
• Bioinformatics_Toolbox

Teaching about phylogenies

• Phylogenetic Investigator
• Phylap
• Dnatree
• SimpleClade

Unix (source code in C or executables)

PC's

... under Windows

... under DOS or in a Windows Command tool "DOS box"

Macintoshes (under Mac OS or Mac OS X)

e-mail or Web servers that can analyze data for you

• Unix (source code in C or executables). I have included programs that are available as C source code because most Unix workstations have a C compiler. (Programs in other compiled languages such as FORTRAN and Pascal, and in interpreted languages such as Java, Perl, Python, or R are also included), as are Java executables. For many of these the programs can also be compiled or run on Windows or Mac OS X systems if they have the appropriate compilers or interpreters loaded.

  PHYLIP PAUP* Phylo_win ODEN TreeTree GCG Wisconsin Package SeqPup Lintre Microsat OSA TREE-PUZZLE AMP fastDNAml MOLPHY PAML SplitsTree PLATO PHYLTEST TreeAlign ClustalW MALIGN GeneDoc COMPARE Seq-Gen TreeTool	GDE sog Phylodendron Treevolve and PTreevolve PSeq-Gen POPTREE gmaes GCUA DERANGE2 LVB BIONJ TAAR ANCML QDate Ctree PASSML TOPALi reticulate RecPars ARB TreeCons Diversi DISTANCE Darwin sendbs	partimatrix BAMBE nneighbor unrooted ROSE weighbor PhyloQuart VeryfastDNAml LARD puzzleboot Willson quartets programs POY RIND TipDate RRTree PAL Mavric dnarates CLINCH Arlequin HY-PHY Genie Vanilla vCEBL TrExMl	PHYCON qclust fastDNAmlRev RevDNArates BRANCHLENGTH TCS CONSEL FORESTER Populations T-REX MrBayes W2H GAPars PAUPRat EDIBLE r8s Mesquite Treefinder PPH MetaPIGA FastME MSA Phylogenetic Tree Drawing APE PHASE	PHYML BEAST TreeView r8s-bootstrap MrBayes tree scanners Hetero Robinson and Foulds distance Clann Jevtrace MrMTgui MrModeltest BootPHYML SymmeTREE TreeJuxtaposer LDDist p4 Porn* TNT Phyl-O-Gen Rhino PIST Phylap Dnatree QuickTree IM
  rnbsp;
  FootPrinter BPAnalysis ProtTest GEODIS TreeScan TreeSetViz ModelGenerator PHYLOGR ProfDist MrAIC Modelfit MCS IQPNNI PARAT ALIFRITZ PhyNav STC TreeSAAP Likewind ELW TreeGraph Supertree scripts Parsimov DPRML Bosque	GeneContent DIVERGE T-Coffee MultiPhyl CBCAnalyzer GHOSTS Tarzan DT-ModSel DualBrothers Notung apTreeshape Multidivtime ParaFit IDC TreeMaker CodonRates BAli-Phy Supertree CoMET galaxie OUCH TreeDyn DigTree Geneious BIRCH	Brownie Mac5 BayesPhylogenies BayesTraits Paloverde HeuristicMRF2 CRANN Kakusan2 PATHd8 MAFFT GARLI TreeStat FigTree PHYSIG scaleboot cBrother RAxML MrBayesPlugin SATCHMO SEMPHY FASTML Rate4Site TopD/fMts Quartet Suite Rainbow	McRate TreeIllustrator HyperTree PhyloBayes Cactus-Pie SWORDS Dendroscope Forest Phylocom TreeMos PhySIC Simprot BEST pcca EREM IDEA indel-Seq-Gen MBEToolbox DTscore PROCOV DART EEEP PhyloCoCo DAWG LEVEL2	PSODA PhyloSort PISE MUSCLE AMBIORE CTree PRAP SeqState HGT NHML SLR rRNA phylogeny AxParafit EvolveAGene3 RPT gtp bootscore TreeToy TreeSnatcher PhyloNet EvolSimulator Concaterpillar GAME DTdraw PHYLLAB
  Bioinformatics_Toolbox NEPAL Codeml3X MULTIDIVTIME HELPER

• PC's
  • as Windows executables (not counting executing in a "DOS box"). Programs available as source code which is Windows-specific are listed here. Java executables are also included. (Note that compilers available on Windows systems, particularly the free Cygwin and MinGW compilers, can also be used to compile many of the programs listed above under Unix generic source code).

    PHYLIP PAUP* TREECON GDA SeqPup MOLPHY WET GeneDoc COMPONENT TREEMAP COMPARE RAPDistance TreeView Phylodendron Fingerprinting II Informatix Software POPGENE TFPGA Ctree GeneTree MVSP RSTCALC Genetix NJplot unrooted Arlequin	DAMBE DnaSP PAML DNASIS MINSPNET BioEdit ProSeq RRTree PAL WINCLADA Nona Phylogenetic Independence vCEBL HY-PHY TreeExplorer Genie Vanilla MEGA TNT GelCompar II Bionumerics TCS FORESTER Populations SiScan	T-REX MrBayes EDIBLE Winboot r8s Mesquite Mgenome Phyledit SYN-TAX PTP DIVA TreeFitter Phylo_win SplitsTree PAST GeneStudio Pro Treefinder PPH MetaPIGA Phyltools MSA APE PHASE PHYML YCDMA	NSA Diversi BEAST Hetero Clann Jevtrace MrMTgui MrModeltest SymmeTREE TreeJuxtaposer Network Discovery Studio Gene Spectronet Phyl-O-Gen Phylap Dnatree IM ProtTest GEODIS TreeSetViz TreeMe ModelGenerator Simplot MDIV PHYLOGR
    ProfDist START MCS IQPNNI STC TreeSAAP Swaap Swaap PH TreeGraph GeneContent DIVERGE MESA MultiPhyl NimbleTree ArboDraw SPAGeDi CBCAnalyzer DualBrothers PaupUp Notung SSA Multidivtime ParaFit IDC TreeMaker	CodonRates BAli-Phy CoMET TreeDyn DigTree Geneious Brownie Mac5 BayesPhylogenies BayesTraits MrEnt SimpleClade CRANN PATHd8 MAFFT GARLI TreeStat FigTree MrBayesPlugin SATCHMO SEMPHY FASTML Rate4Site Quartet Suite Rainbow	aLRT McRate TreeIllustrator HyperTree SWORDS GeoPhyloBuilder Dendroscope Phylocom TreeMos TOPALi Simprot BEST pcca EREM MBEToolbox DTscore EEEP LEVEL2 PSODA PhyloSort RAxML MUSCLE CTree PRAP SeqState	Leaphy GRate SLR rRNA phylogeny FAMD AxParafit DTscore PROCOV DART EEEP PhyloCoCo DAWG EvolveAGene3 Bosque TreeToy TreeSnatcher PhyloNet GAME

  • under DOS (MSDOS, PCDOS) or in a Command Tool "DOS box" in Windows

    PHYLIP PAUP* MEGA Hennig86 MEGA RA Nona TREECON Microsat DISPAN RESTSITE NTSYSpc METREE Hadtree, Prepare and Trees PHYLTEST RAPDistance DIPLOMO TREE-PUZZLE ClustalW MALIGN GeneDoc COMPARE CMAP Random Cladistics CoSta

    POPTREE GEOMETRY PDAP PICA REDCON TAXEQ3 BIONJ ANCML REAP MVSP Lintre T-REX sendbs K2WuLi weighbor POY TreeDis Network CLINCH Gambit qclust CONSEL LVB PAUPRat

    FSTAT SYN-TAX FastME MSA QDate Robinson and Foulds distance DIVAGE BPAnalysis TreeScan Genepop Kakusan2

• Macintosh Mac OS or Mac OS X executables. Programs available in source code that is Mac OS X specific are included. Java executables are also included. (Note that most of the programs in the Unix/Linux list above can also be compiled for Mac OS X using the GCC compiler that is distributed with Mac OS X).

  PHYLIP PAUP* CAFCA MacT TreeTree SeqPup Microsat TREE-PUZZLE fastDNAml MacClade Spectrum SplitsTree PLATO AutoDecay ClustalW TREEMAP CAIC COMPARE Bi-De Seq-Gen CONSERVE TreeView NJplot DendroMaker MUST 2000	DNA Stacks Phylogenetic Investigator Tree Draw Deck Phylodendron TreeRot Treevolve and PTreevolve PSeq-Gen Fingerprinting II Informatix Software BIONJ GCUA ACAP GeneTree QDate LVB T-REX unrooted GeneStrut COMPONENT Lite weighbor Modeltest PAML LARD Willson quartets programs ALIGN CodonBootstrap	DNASIS TipDate RRTree MacroCAIC PAL RadCon TreeEdit Arlequin vCEBL HY-PHY TreeThief Genie Vanilla TCS MrBayes FORESTER PAUPRat r8s GDA Mesquite SYN-TAX DIVA TreeFitter Phylo_win Treefinder	PPH MetaPIGA MSA PHYML BEAST Hetero Robinson and Foulds distance Clann Jevtrace MrModeltest BootPHYML SymmeTREE TreeJuxtaposer MacVector SIMMAP TNT Phyl-O-Gen Rhino PIST Phylap Dnatree ProtTest GEODIS TreeScan TreeSetViz	ModelGenerator PHYLOGR ProfDist MCS IQPNNI TreeSAAP Permute! MESA MultiPhyl SGRunner DualBrothers Notung Cadence ParaFit TreeMaker BAli-Phy Supertree CoMET TreeDyn Geneious Brownie Mac5 BayesPhylogenies BayesTraits Paloverde	CRANN MAPPS PATHd8 MAFFT GARLI TreeStat FigTree MrBayesPlugin SEMPHY Quartet Suite Rainbow TreeIllustrator HyperTree Kakusan2 SWORDS Dendroscope Phylocom TreeMos PhySIC TOPALi BEST pcca indel-Seq-Gen PhyloCoCo LEVEL2
  PSODA PhyloSort RAxML MUSCLE CTree PRAP SeqState SLR AxParafit EvolveAGene3 TreeToy TreeSnatcher PhyloNet GAME GenoDive

Microsatellite data

• RSTCALC
• POPTREE
• Microsat
• Populations
• MSA
• YCDMA
• Network
• IM

RAPDs, RFLPs, or AFLPs

• tfpga
• RAPDistance
• Fingerprinting II Informatix Software
• GelCompar II
• Bionumerics
• Winboot
• REAP
• RESTSITE
• MVSP
• DENDRON
• Phyltools
• Network
• BIRCH
• FAMD

Continuous quantitative characters

• PHYLIP
• Mesquite
• ANCML
• COMPARE
• CMAP
• PDAP
• ACAP
• Phylogenetic Independence
• APE
• CAIC
• TreeScan
• PHYLOGR
• IDC
• CoMET
• OUCH
• Brownie
• BayesTraits
• TNT
• PHYSIG
• Cactus-Pie
• pcca
• RPT

Gene frequencies (aside from microsatellite loci)

• PHYLIP
• DAMBE
• DISPAN
• GDA
• POPGENE
• YCDMA
• FSTAT
• Arlequin
• DnaSP
• APE
• DIVAGE
• GeneStrut
• POPTREE
• Genepop
• SPAGeDi
• RPT
• GenoDive

Here are the packages that have most recently been added to these listings: (the most recent ones first). Entries are retained in this list for about 6 months. Note also below the "waiting list" area listing programs that are to be added. You can use the submission form here to submit new entries.

MULTIDIVTIME HELPER (26 April 2008) prepares constraint trees and folders for Multidivtime GenoDive (25 April 2008) computes genetic diversity measures including standardized distances. Codeml3X (19 April 2008) script to run CODEML from PAML three times with different values of ω NEPAL (19 April 2008) infers networks by parsimony or likelihood. PHYLLAB (12 April 2008) A MATLAB toolbox for MCMC Bayesian inference of phylogenies from sequences. Bioinformatics_Toolbox (12 April 2008) A sequence analysis MATLAB toolbox which can make distance-based trees. DTdraw (5 April 2008) draws gene duplication history trees. GAME (5 April 2008) estimates the α shape parameter using distances and also infers the tree. Concaterpillar (29 March 2008) performs a hierarchical likelihood ratio test for phylogenetic congruence. EvolSimulator (29 March 2008) simulates sequence evolution with genomic events and lateral gene transfer as well. PhyloNet (23 March 2008) infers networks by a parsimony method allowing recombinations. TreeSnatcher (22 March 2008) captures trees from graphic images. TreeToy (15 March 2008) displays and reroots trees, and selects subtrees. bootscore (9 March 2008) computes majority rule consensus tree and puts bootstrap scores on it. gtp (9 March 2008) gene tree parsimony program. RPT (1 March 2008) makes circular plots of a tree that show the values of characters graphically. EvolveAGene3 (23 February 2008) simulates evolution of protein sequences with gaps AxParafit (16 February 2008) Parallel and optimized version of the ParaFit program for host-parasite analyses. FAMD (15 February 2008) Distance and distance matrix programs for RAPD fingerprinting with consensus and bootstraps. rRNA phylogeny (9 February 2008) phylogenies from compensating substitutions for paired and unpaired rRNA sites. SLR (9 February 2008) sitewise analysis of nonsynonymous / synonymous rates of substitution. NHML (2 February 2008) Infers maximum likelihood phylogenies using a nonhomogenous model of nucleotide change. Leaphy (2 February 2008) infers maximum likelihood phylogenies by its own search methods. HGT (26 January 2008) estimates the rate of horizontal gene transfer. GRate (26 January 2008) does relative rate tests comparing prespecified groups using PAUP* SeqState (19 January 2008) recodes indels in various ways. PRAP (19 January 2008) implements ratchet searches and Bremer support calculations in PAUP* CTree (12 January 2008) interactively views clusters according to measures of their diversity. AMBIORE (12 January 2008) estimates rates of change of bases dependent on the bases at the two neighboring sites. MUSCLE (11 December 2007) multiple sequence alignment using trees. PISE (3 December 2007) generates web interfaces from XML for molecular evolution programs. PhyloSort (3 December 2007) finds monophyletic groups with particular subsets of species in trees. PSODA (24 November 2007) parsimony program for nucleotide sequences. LEVEL2 (24 November 2007) constructs networks with limited degrees of looping from triplets. DAWG (17 November 2007) simulates evolution of DNA sequences with recombination and gaps. GRIMM server (17 November 2007) computes distances or phylogenies that minimize chromosome rearrangements. PhyloCoCo (11 November 2007) infers model parameters and uses special search methods to find the maximum likelihood tree. EEEP (11 November 2007) reconstructs horizontal gene transfer events from a gene tree and a species tree. PROCOV (4 November 2007) does maximum likelihood inference for proteins under covarion models. DART (4 November 2007) a package with methods for RNA structure and sequence alignment. DTscore (27 October 2007) a distance-based program to reconstruct phylogenies of tandem duplication copies. MBEToolbox (27 October 2007) a MATLAB toolbox to analyze DNA and protein sequences.

• There is one phylogeny software list even more complete and up-to-date than this one: a more recent version of this list. If you are reading this on the web pages at our server evolution.gs.washington.edu, you are reading the most up-to-date version. But if you are reading a version stored anywhere else, you might want to look here instead.
• The Institut Pasteur in Paris has the Bio NetBook, a search facility for biocomputing web pages, which include web pages of other lists, web pages of programs or servers, and some pages that simply no longer exist. It is located at http://www.pasteur.fr/recherche/BNB/bnb-en.html. Programs for phylogenies can be found by, for example, selecting software from the Resource Type list and evolution from the Biological Domain list without selecting any Organism. Other categories worth looking at include Online Analysis Tools, Sequence Analysis and Bio-computing.
• Sergios-Orestis Kolokotronis has posted an extensive table of phylogeny programs at his site at the American Museum of Natural History, and near it are others under headings such as "molecular evolution" and "alignment".
• Classification and clustering programs are described in a useful Web page maintained by Fionn Murtagh at http://astro.u-strasbg.fr/~fmurtagh/mda-sw/online-sw.html. Note, however, that inferring phylogenies and making clusters are different tasks; the software described on that list will be of most use to people who are trying to cluster or classify but not as much for inferring phylogenies.
• The Digital Taxonomy web site, maintained by Mauro José Cavalcanti in Rio de Janeiro, Brazil, lists phylogeny programs (and programs in other areas of systematics and morphometrics), with attention restricted to those that are free and whose source code is publicly available.
• Genamics, a company located in Hamilton, New Zealand, maintains the SoftwareSeek searchable index of bioinformatics software at http://genamics.com/software/index.htm in a number of categories. One of them is Phylogenetic Analysis. They have a reasonably large number of entries under that heading, though it also includes some statistical genetics software that is really not phylogenetic. Their listing has links to the web sites of the software; for those programs that are not available by Web they maintain copies for download at their server.
• Georg Fuellen at the University of Bielefeld, Germany, has a very good page on Multiple Alignment Resources at http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html.
• David Robertson of the Bioinformatics Education and Research at the University of Manchester, England, maintains a very informative web site at listing programs and their web sites that test for the presence of recombination or hybridization events in DNA sequence data. It lists some programs that are covered here, and others that are outside the scope of these web pages. That site is located at http://bioinf.man.ac.uk/~robertson/recombination/.
• Mike Robeson at the University of Colorado maintains a page with multiple programs listed as Bioinformatics software for Mac OS X.
• The Bioinformatics Organization, a nonprofit group in Hudson, Massachusetts, has posted the bioinformatics.org web pages. These offer a free membership and host open source software projects in bioinformatics. They also have a Molecular Linux listing of Linux programs to carry out bioinformatics tasks.
• Don Gilbert, of the Department of Biology of the University of Indiana, has a good web page on Free Software in Molecular Biology for Macintosh and MS Windows computers as of 1998 at http://iubio.bio.indiana.edu/soft/molbio/Listings.html. It lists some popular packages and all packages and programs kept at the IUBio ftp server at that time (see our description of that server). Unfortunately the web links on that page are not active so the addresses must be retyped by hand.
• Andrea Ramge, of Biomax Informatics AG, Martinsried, Germany has created the bioinformatik.de index of resources. It includes a list of software located at http://www.bioinformatik.de/cgi-bin/browse/Catalog/Software. The phylogeny programs listings there are located within the categories for different operating systems.
• Biodirectory.com maintains a BioWiki site, with content edited by users. It requires a free login and is supported by advertising. It has lists of phylogeny and alignment programs.
• Silvio Nihei at the University of São Paulo in Brazil has produced a list: Programas para Filogenia (Morfológica) e Biogeografi in Portugese. It concentrates on a small number of programs that mostly use parsimony methods.

This is a "waiting list" showing links to the web pages of many new phylogeny programs, which I have not yet had time to add to the main listing. They will be listed there, with a single web link and no detailed explanation. I hope that this list will gradually shrink as the new programs are put into the main listing. You can use the submission form here to submit new entries.

These are waiting to be added:

• Tree Tracker detects overrepresented clusters in trees.
• Ultrametric Check calculates root-to-tip distances for all species in a tree.
• analysis molecular population genetics package can compute Kimura 2-parameter distances.
• CIPRES Web Portal server runs parsimony, likelihood and Bayesian programs.
• CodeAxe estimates neighbor-dependent mutation rates in DNA sequences.