Methods

By computer

Cross-referenced

Data types

Web servers

New programs

Submitting

Changes

Waiting list

Other lists

Old programs

Not listed

News

Here are 392 phylogeny packages and 54 free web servers, (almost) 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 monthly. 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
• EMBOSS
• phangorn
• Bio++
• ETE
• DendroPy
• SeaView
• Crux

Parsimony programs

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

Mesquite PAST FootPrinter BPAnalysis Simplot Parsimov NimbleTree PaupUp Notung BIRCH IDEA PSODA PRAP SeqState Bosque PhyloNet EMBOSS phangorn Murka Freqpars SeaView PAUPRat

Distance matrix methods

PHYLIP PAUP* MEGA MacT ODEN TREECON DISPAN RESTSITE NTSYSpc METREE GDA SeqPup PHYLTEST Lintre Phylo_win POPTREE2 Gambit gmaes DENDRON BIONJ TFPGA MVSP ARB Darwin

T-REX sendbs nneighbor DAMBE weighbor DNASIS MINSPNET PAL Arlequin PEBBLE HY-PHY Vanilla GelCompar II Bionumerics qclust TCS Populations Winboot SYN-TAX PTP SplitsTree FastME APE MacVector QuickTree

Simplot ProfDist START2 STC NimbleTree CBCAnalyzer PaupUp Geneious BIRCH SEMPHY FASTML Rate4Site SWORDS IDEA FAMD Bosque GAME Bioinformatics_Toolbox TreeFit EMBOSS phangorn PC-ORD Bio++ UGENE NINJA

SeaView Statio TIMER Crux Ancestor ANC-GENE Bn-Bs

Computation of distances

PHYLIP PAUP* RAPDistance MULTICOMP Microsat DIPLOMO OSA DISPAN RESTSITE NTSYSpc TREE-PUZZLE GCUA DERANGE2 POPGENE TFPGA REAP MVSP RSTCALC Genetix DISTANCE Darwin sendbs 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 START2 Swaap Swaap PH SPAGeDi

CBCAnalyzer PaupUp SEMPHY SWORDS rRNA phylogeny FAMD GAME Bioinformatics_Toolbox GenoDive analysis TreeFit EMBOSS Murka Bio++ UGENE POPTREE2 DISTREE SeaView Crux Bn-Bs HON-new

Maximum likelihood methods

PHYLIP PAUP* fastDNAml MOLPHY PAML Spectrum SplitsTree TREE-PUZZLE SeqPup Phylo_win PASSML ARB Darwin Modeltest DAMBE PAL dnarates HY-PHY Vanilla DT-ModSel Bionumerics fastDNAmlRev RevDNArates rate-evolution CONSEL

EDIBLE PLATO Mesquite PTP Treefinder MetaPIGA RAxML PHYML r8s-bootstrap MrMTgui MrModeltest BootPHYML PARBOOT p4 Porn* SIMMAP Spectronet Rhino TipDate ProtTest ModelGenerator Simplot MrAIC Modelfit IQPNNI

PARAT ALIFRITZ PhyNav DPRML MultiPhyl NimbleTree PaupUp SSA CoMET BIRCH Mac5 Kakusan4 GARLI PHYSIG SEMPHY FASTML Rate4Site aLRT McRate EREM PROCOV DART PhyloCoCo PRAP

SeqState Leaphy NHML SLR rRNA phylogeny Bosque Concaterpillar PHYLLAB NEPAL EMBOSS CodeAxe phangorn Bio++ FastTree nhPhyML PhyML-Multi Segminator raxmlGUI MixtureTree SeaView GZ-Gamma PAUPRat Crux

Bayesian inference methods

PAML BAMBE PAL Vanilla MrBayes Mesquite PHASE BEAST MrBayes tree scanners p4 SIMMAP IMa2 BAli-Phy BayesPhylogenies MrBayesPlugin PhyloBayes PHASE Cadence Multidivtime BEST AMBIORE PHYLLAB bms_runner tracer burntrees

Bio++ Crux ANC-GENE

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
• EMBOSS

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 MESA BIRCH SimpleClade

Dendroscope Forest Phylocom TreeToy Bioinformatics_Toolbox Phyutility EMBOSS PhyloWidget Phybase ETE TreeGraph 2 Crux

Looking for hybridization or recombination events

RecPars TOPALi partimatrix Network TCS T-REX PLATO PPH Spectronet IMa2 Simplot START2 Likewind DualBrothers cBrother EEEP HGT PhyloNet EvolSimulator Concaterpillar PhyML-Multi RDP3

Bootstrapping and other measures of support (for Bayesian support methods see the Bayesian inference list above).

PHYLIP PAUP* Random Cladistics AutoDecay TreeRot DNA Stacks OSA DISPAN PHYLTEST Lintre sog POPTREE2 MEGA PARBOOT PICA ModelTest TAXEQ3 BAMBE DAMBE puzzleboot CodonBootstrap Gambit PAL 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* ProtTest ModelGenerator Simplot Permute! ELW

MultiPhyl GHOSTS PaupUp Geneious BIRCH BayesPhylogenies scaleboot aLRT PhyloBayes SWORDS CTree PRAP FAMD PhyloNet PHYLLAB Phyutility EMBOSS FastTree Bionumerics tracer burntrees Bio++ raxmlGUI MixtureTree

Compatibility analysis

• COMPROB
• PHYLIP
• PICA
• partimatrix
• PPH
• Spectronet
• BIRCH
• EMBOSS
• Murka
• Phybase
• TIGER

Consensus trees, subtrees, supertrees, and distances between trees

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

EEEP PhyloSort FAMD Phyutility EMBOSS phangorn Murka RAxML Phybase iGTP raxmlGUI Crux

Tree-based sequence alignment

• TreeAlign
• ClustalW
• MALIGN
• GeneDoc
• DAMBE
• POY
• ALIGN
• DNASIS
• FootPrinter
• ALIFRITZ
• T-Coffee
• ArboDraw
• BAli-Phy
• Geneious
• BIRCH
• MAFFT
• LOBSTER
• DART
• MUSCLE
• Bosque
• EMBOSS
• SeaView
• SuiteMSA

Gene duplication and genomic analysis

• DERANGE2
• FORESTER
• BPAnalysis
• Notung
• TopD/fMts
• DTscore
• DART
• gtp
• EvolSimulator
• DTdraw
• Mgenome
• Tree Tracker
• bms_runner
• MANTiS
• ETE
• MANTiS
• iGTP

Biogeographic analysis and host-parasite comparison

• COMPONENT
• TREEMAP
• DIVA
• TreeFitter
• GEODIS
• Tarzan
• ParaFit
• Phylocom
• AxParafit
• GenGIS
• S-DIVA
• Lagrange
• CoRe-PA
• Jane

Comparative method analysis

PHYLIP CAIC COMPARE PDAP ANCML RIND MacroCAIC Phylogenetic Independence MacClade Mesquite APE Jevtrace SIMMAP PHYLOGR TreeSAAP Permute! Parsimov DIVERGE IDC OUCH BIRCH BayesTraits PHYSIG Cactus-Pie

Phylocom pcca EMBOSS bms_runner SLOUCH Phybase

Simulation of trees or data

COMPONENT Seq-Gen Treevolve and PTreevolve PSeq-Gen COMPARE ROSE PAML ProSeq PAL Vanilla MacClade EDIBLE Mesquite Treefinder Network Phylogen MESA SGRunner apTreeshape Simprot EREM indel-Seq-Gen DAWG EvolveAGene3

EvolSimulator Bio::Phylo Recodon NetRecodon SuiteMSA Crux

Examination of shapes of trees

• MacroCAIC
• Genie
• PAL
• Vanilla
• RadCon
• BRANCHLENGTH
• APE
• Tracer
• SymmeTREE
• TreeScan
• MESA
• apTreeshape
• TreeStat
• CTree
• Phyutility
• laser
• PhyRe
• Bio::Phylo

Clocks, dating and stratigraphy

PHYLIP QDate Modeltest PAML RRTree PEBBLE TreeEdit HY-PHY MEGA PAL rate-evolution BRANCHLENGTH r8s PAST Treefinder Network APE BEAST MrMTgui MrModeltest SymmeTREE Porn* TipDate Rhino GHOSTS Cadence

Multidivtime CodonRates BIRCH Brownie PATHd8 McRate PhyloBayes Cactus-Pie GRate NHML TreeFit PHYLTEST Murka TIMER

Model Selection

• Modeltest
• MrMTgui
• MrModeltest
• Porn*
• ModelGenerator
• ProtTest
• MrAIC
• Modelfit
• DT-ModSel
• BayesTraits
• Kakusan4
• MAPPS
• DART
• Concaterpillar
• Statio
• jMODELTEST

Description or prediction of data from trees

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

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 2 ArboDraw PaupUp Notung TreeDyn DigTree Geneious BIRCH Paloverde MrEnt FigTree HyperTree GeoPhyloBuilder Dendroscope CTree TreeToy TreeSnatcher Plus DTdraw PHYLLAB Bioinformatics_Toolbox EMBOSS PhyloWidget GenGIS Bio++ Bio::Phylo

S-DIVA UGENE ETE POPTREE2 Segminator MixtureTree SeaView Archaeopteryx SuiteMSA

Sequence management/job submission

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

EMBOSS PyCogent PHYDIT Segminator SeaView SuiteMSA

Teaching about phylogenies

• Phylogenetic Investigator
• Phylap
• Dnatree
• SimpleClade

Unix (source code in C or executables)

Multiplatform interpreters (Java, Perl, Python, R, MATLAB)

PC's

... under Windows

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

Macintoshes (under Mac OS X or Mac OS)

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 SeqPup Lintre Microsat OSA TREE-PUZZLE fastDNAml MOLPHY PAML SplitsTree PHYLTEST TreeAlign ClustalW MALIGN GeneDoc COMPARE Seq-Gen TreeTool GDE sog Phylodendron Treevolve and PTreevolve	PSeq-Gen POPTREE2 gmaes GCUA DERANGE2 LVB BIONJ ANCML QDate PASSML TOPALi RecPars PARBOOT ARB DISTANCE Darwin sendbs partimatrix BAMBE nneighbor unrooted ROSE weighbor PhyloQuart puzzleboot	Willson quartets programs POY RIND RRTree Mavric dnarates Arlequin HY-PHY Genie Vanilla qclust fastDNAmlRev RevDNArates BRANCHLENGTH TCS CONSEL FORESTER Populations T-REX MrBayes W2H GAPars EDIBLE	r8s Mesquite Treefinder PPH PLATO MetaPIGA FastME MSA Phylogenetic Tree Drawing APE PHASE PHYML BEAST TreeView r8s-bootstrap MrBayes tree scanners Robinson and Foulds distance Clann Jevtrace MrMTgui MrModeltest BootPHYML SymmeTREE TreeJuxtaposer LDDist	p4 Porn* TNT Phylogen Rhino TipDate Phylap Dnatree QuickTree IMa2 FootPrinter BPAnalysis ProtTest GEODIS TreeScan TreeSetViz ModelGenerator PHYLOGR ProfDist MrAIC Modelfit IQPNNI PARAT ALIFRITZ PhyNav
  STC TreeSAAP Likewind ELW TreeGraph 2 Supertree scripts Parsimov Bosque DIVERGE T-Coffee CBCAnalyzer GHOSTS Tarzan DT-ModSel DualBrothers apTreeshape Multidivtime Mgenome ParaFit IDC TreeMaker CodonRates	BAli-Phy Supertree OUCH TreeDyn DigTree Geneious BIRCH Brownie Mac5 BayesPhylogenies BayesTraits Paloverde HeuristicMRF2 CRANN Kakusan4 PATHd8 MAFFT GARLI TreeStat FigTree PHYSIG scaleboot cBrother RAxML	MrBayesPlugin LOBSTER SEMPHY FASTML Rate4Site TopD/fMts Quartet Suite Rainbow McRate HyperTree PhyloBayes Cactus-Pie SWORDS Dendroscope Forest Phylocom PhySIC_IST Simprot BEST pcca EREM indel-Seq-Gen MBEToolbox DTscore	PROCOV DART EEEP DAWG LEVEL2 PSODA PhyloSort PISE MUSCLE AMBIORE CTree PRAP HGT NHML SLR rRNA phylogeny AxParafit EvolveAGene3 gtp TreeToy TreeSnatcher Plus EvolSimulator	Concaterpillar GAME DTdraw NEPAL PHYLLAB Bioinformatics_Toolbox Tree Tracker analysis CodeAxe Phyutility EMBOSS phangorn FastTree PhyloWidget laser bms_runner tracer burntrees SLOUCH Murka MANTiS Freqpars GenGIS CONSERVE Bio++
  UGENE DISTREE Phybase ETE PyCogent DendroPy CAIC NINJA MUST nhPhyML PhyML-Multi Segminator iGTP Bio::Phylo Recodon NetRecodon Lagrange CoRe-PA MixtureTree TIGER SeaView Jane GZ-Gamma PAUPRat Archaeopteryx	SuiteMSA Crux Ancestor ANC-GENE Bn-Bs HON-new

• Multiplatform interpreters (Java, Perl, Python, R, MATLAB). These are programs that are written in a language that is interpreted, step by step, in real time by a computing environment that can run on many different operating systems.

  (I am just starting to list interpreter code here. Until recently it was listed under Unix, Windows and/or Mac OS X). Until I finish transferring interpreter code here this list will be incomplete, and you will find many programs written in interpreted languages there).

  Java

  • PAL
  • Mesquite
  • BIRCH
  • PRAP
  • SeqState
  • TCS
  • IDEA
  • PhyloNet
  • Notung
  • Vanilla
  • NINJA
  • qclust
  • PEBBLE
  • SplitsTree
  • SeqPup
  • DPRML
  • MultiPhyl
  • Treefinder
  • PhyloCoCo
  • ProtTest
  • CoMET
  • Segminator
  • jMODELTEST

• 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). Programs run in interpreted environments such as Perl, Python, R or MATLAB can also be run under Windows if the proper environment is installed. These programs are listed above under Unix.

    PHYLIP PAUP* TREECON GDA SeqPup MOLPHY GeneDoc COMPONENT TREEMAP COMPARE RAPDistance TreeView Phylodendron POPGENE TFPGA GeneTree MVSP RSTCALC Genetix NJplot unrooted Arlequin DAMBE DnaSP PAML	DNASIS MINSPNET BioEdit ProSeq WINCLADA NONA Phylogenetic Independence HY-PHY TreeExplorer Genie MEGA TNT GelCompar II Bionumerics FORESTER Populations T-REX MrBayes EDIBLE Winboot r8s	Mesquite Phyledit SYN-TAX PTP DIVA TreeFitter Phylo_win PAST GeneStudio Pro Treefinder PPH MetaPIGA Phyltools MSA Mgenome APE PHASE PHYML YCDMA NSA BEAST Clann Jevtrace MrMTgui	MrModeltest SymmeTREE TreeJuxtaposer Network Spectronet Phylogen Phylap Dnatree IMa2 ProtTest GEODIS TreeSetViz TreeMe ModelGenerator Simplot PHYLOGR ProfDist START2 IQPNNI STC TreeSAAP Swaap Swaap PH TreeGraph 2 DIVERGE	MESA NimbleTree ArboDraw SPAGeDi CBCAnalyzer DualBrothers PaupUp SSA Multidivtime ParaFit IDC TreeMaker CodonRates BAli-Phy TreeDyn DigTree Geneious Brownie Mac5 BayesPhylogenies BayesTraits MrEnt
    SimpleClade CRANN PATHd8 MAFFT GARLI TreeStat FigTree MrBayesPlugin LOBSTER SEMPHY FASTML Rate4Site Quartet Suite Rainbow aLRT McRate HyperTree SWORDS GeoPhyloBuilder Dendroscope Phylocom TOPALi Simprot BEST pcca	EREM MBEToolbox DTscore EEEP LEVEL2 PSODA PhyloSort RAxML MUSCLE CTree PRAP Leaphy GRate SLR rRNA phylogeny FAMD AxParafit DTscore PROCOV DART EEEP CONSERVE DAWG	EvolveAGene3 Bosque TreeToy TreeSnatcher Plus GAME TreeFit FastTree PhyloWidget tracer Murka MANTiS PC-ORD GenGIS Bio++ S-DIVA UGENE Phybase ETE Cactus-Pie PHYDIT POPTREE2 RDP3 PhyRe	Segminator iGTP Recodon NetRecodon CoRe-PA TIGER SeaView Jane TIMER HON-new

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

    PHYLIP PAUP* MEGA Hennig86 MEGA RA NONA TREECON Microsat DISPAN RESTSITE NTSYSpc METREE PHYLTEST RAPDistance DIPLOMO TREE-PUZZLE ClustalW MALIGN GeneDoc Random Cladistics POPTREE2 GEOMETRY PDAP PICA

    REDCON TAXEQ3 BIONJ ANCML REAP MVSP Lintre T-REX sendbs weighbor POY TreeDis Network Gambit CONSEL LVB FSTAT SYN-TAX FastME MSA QDate Robinson and Foulds distance DIVAGE BPAnalysis

    TreeScan Genepop Kakusan4 DISTREE GZ-Gamma PAUPRat Statio Ancestor ANC-GENE Bn-Bs

• Macintosh Mac OS X or Mac OS executables. 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). Programs run in the interpreted environments Perl and Python can also be run in Mac OS X as these are included in the Mac OS X distribution. We have not yet included these in the list below but should. R or MATLAB can also be run under Mac OS X if the proper environment is installed. These programs are listed above under Unix.

  PHYLIP PAUP* MacT SeqPup Microsat TREE-PUZZLE fastDNAml MacClade Spectrum AutoDecay CAFCA ClustalW TREEMAP CAIC COMPARE Seq-Gen CONSERVE TreeView NJplot DendroMaker MUST DNA Stacks Phylogenetic Investigator Tree Draw Deck	Phylodendron TreeRot Treevolve and PTreevolve PSeq-Gen BIONJ GCUA GeneTree QDate LVB T-REX unrooted COMPONENT Lite weighbor Modeltest PAML Willson quartets programs ALIGN CodonBootstrap DNASIS PLATO MacroCAIC RadCon TreeEdit Arlequin	HY-PHY TreeThief Genie MrBayes FORESTER r8s GDA Mesquite SYN-TAX DIVA TreeFitter Phylo_win Treefinder PPH MetaPIGA MSA PHYML BEAST Robinson and Foulds distance Clann Jevtrace MrModeltest	BootPHYML SymmeTREE TreeJuxtaposer MacVector SIMMAP TNT Phylogen Rhino TipDate Phylap Dnatree ProtTest GEODIS TreeScan TreeSetViz ModelGenerator PHYLOGR ProfDist IQPNNI TreeSAAP Permute! MESA SGRunner DualBrothers	Cadence ParaFit TreeMaker BAli-Phy Supertree TreeDyn Geneious Brownie Mac5 BayesPhylogenies BayesTraits Paloverde CRANN MAPPS PATHd8 MAFFT GARLI TreeStat FigTree MrBayesPlugin SEMPHY Quartet Suite Rainbow	HyperTree Kakusan4 SWORDS Dendroscope Phylocom PhySIC_IST TOPALi BEST pcca indel-Seq-Gen PhyloCoCo LEVEL2 PSODA PhyloSort RAxML MUSCLE CTree PRAP SLR AxParafit EvolveAGene3 TreeToy TreeSnatcher Plus
  GAME GenoDive PhyloWidget tracer MANTiS GenGIS Bio++ UGENE Phybase ETE PyCogent DendroPy NEPAL Bosque TreeGraph 2 Segminator iGTP Bio::Phylo Recodon Lagrange NetRecodon CoRe-PA TIGER SeaView	Jane PAUPRat SuiteMSA

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 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.

(List is currently empty because I have been unable to do much updating owing to other pressures so no new packages have been added in the last year).

• 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.
• 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".
• Wikipedia has a good list of sequence alignment software (including both tree-based and non-tree-based alignment methods) here at http://en.wikipedia.org/wiki/List_of_sequence_alignment_software
• 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/programs.shtml.
• 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, which can be sorted by keywords.
• On Wikipedia there is a List of phylogenetic tree visualization software at http://en.wikipedia.org/wiki/List_of_phylogenetic_tree_visualization_software
• The University of California Museum of Paleontology page of Phylogenetics Software Resources at http://www.ucmp.berkeley.edu/subway/phylo/phylosoft.html. A few programs are listed, but there is a very nice list of software lists there.
• 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. The phylogeny software is under "Phylogenetic Analysis" within each operating system.
• Richard Christen at the Université de Nice, France, has a list of Tree and Tree-software for visualisation and manipulations dealing with phylogenetic trees at http://bioinfo.unice.fr/biodiv/Tree_editors.html
• Silvio Nihei at the University of São Paulo in Brazil has produced a list: Programas para Filogenia in Portugese. It concentrates on a small number of programs that mostly use parsimony methods.

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. Unfortunately, the links to the software are very out of date and few of them work.

---

New programs waiting to be added

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:

This bunch are all old programs from Masatoshi Nei's lab, available from the same web page there

• ADAPTSITE, intended to estimate positive and negative selection at a single amino acid site.

These are not from the Nei site:

• PhyRe infers adequacy of taxon sampling for phylogenetic studies.
• phylobase is an R package that contains a class of functions for comparative methods, incorporating one or more trees and trait data.
• PhyML-mixtures, a PhyML version for mixture of amino acid models (EX2, EX3, EHO, UL2, and UL3).
• PhyD*, Fast NJ-like algorithms to deal with incomplete distance matrices.
• SDM a fast distance-based approach for tree and supertree building in phylogenomics.
• SSIMUL does speciation signal extraction from multigene families.
• Clearcut carries out Relaxed Neighbor Joining (RNJ), a faster NJ-like distance method.
• MP-EST (also described here) uses trees from different loci to infer a species tree by a pseudo-maximum-likelihood method.
• TreeRogue, an R script for getting trees from published figures of them.
• Serial NetEvolve simulation program evolves serially-sampled sequences with or without recombination.
• Rococo reconstructs ancestral gene clusters for a multigene family on a given tree.

I will be adding new programs as they come in, and removing programs from this waiting list as they are added to the main listing. You can speed up the listing of a program and help me by using the submission form here to submit entries. Any entries submitted that way (including ones that are already in the Waiting List) will "jump the queue" and get highest priority for being added to the full listing.

---

News

• (27 May 2012) Adding one entry from the Waiting List each week, have caught up with submissions submitted through the web form, and am populating a new column in the cross-referenced table, one for multiplatform interpreted code such as Java, Perl, Python, R, and MatLab. The Java programs are entered in that column. After this I will put the others in it, then go back to the main Phylogeny Programs front web page and put in a software category for these interpreters. If you have a new program, or an old one that I don't list, don't wait for me to find it by myself -- I still don't have time to, so use the web submission form.
• (19 March 2012) Well, I should have known that another quarter of teaching lay ahead. Now that is done and I should make gradual progress over the next two quarters.
• (23 December 2011) Once again I got stalled by heavy teaching. Now resuming again and hope to gradually catch up. One puzzle is how to handle R packages. There are a great many of them, and most are not listed here yet. It simply is too much work for me to track them all down, figure out their features, and make an entry for each one. So I will put in only those whose authors use our submission form to help create the entry.
• (20 August 2011) I have resumed adding new submissions that people sent in using our software submission forms -- there are about 10 waiting, some having waited for over 6 months. Apologies for that, I was busy teaching and desperately trying to write up old results. I hope to gradually add all 10 over the next month or so, one at a time.
• (17 December 2010) I have started (on this 107th anniversary of the Wright Brothers' famous first flight) this News section of the page. The current status is that I have completed (over the past 2-3 years) a complete pass through the listings, updating them. However of course some may have become outdated since then. Ahead is adding new entries, of which I expect there to be 30-40. I am caught up on entries that were submitted by the web submission form.
• (19 December 2010) I have finished adding the ones that were already in our Waiting List. Now to take some of the approximately 40 leads that I have accumulated and put entries for the relevant ones into the Waiting List.
• (19 June 2014) Things have been stalled for some years but now I am gradually (and slowly) resuming adding and correcting entries. Please keep using the software submission form, and please be patient. I was stalled owing to needing to write grants, and owing to not getting them so I now have no programming assistance. Progress to being current will be slow. If you are impatient, how about volunteering to help? We could set up some web site accessible to a team.

Mysteries you can help us solve

These haven't been entered because I am not sure what they do and whether it is covered by this list. Anyone with relevant information should let me know.

• 3item extracts 3-item statements from "areagrams", whatever that means, but can only be accessed by joining their Yahoo group. So I don't really know what it does.
• Dependency v2.1 uses Multiple Interdependency to detect functional interactions between amino acids in proteins. Does not seem to actually use a phylogeny.
• Codep Maximizes co-evolutionary interdependencies to discover interacting proteins. Also does not seem to actually use a phylogeny.
• PhyloGrapher shows clustering relationships between genes in a genome based on a distance matrix. But is it a phylogeny program?
• Phylosopher commercial package for functional genomics said to include some phylogeny functions. Does it?
• Phylogenator server displaying aligned sequences -- does it actually use or construct phylogenies?
• MultiLocus calculates multiple-locus measures of population differentiation from population genetic data. But unless someone can show me that it can calculate a measure of distance between two populations within a data set, it does not seem appropriate for this list.
• CIPRES-KEPLER Java-based framework for organizing workflow and submitting jobs. I am not sure whether any specifically phylogeny-based pieces have yet been supplied with this.

      Until I get more information these programs cannot be further listed.

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