Phylogeny programs by method and system

This table lists packages by method (down the side of the table) cross-referenced with systems on which the programs work (across the top). It includes distributed software, but not webserver services. I have used the descriptions provided by the authors of the packages where possible, but errors and omissions are entirely possible. If you see any, please e-mail me at (joe (at) gs.washington.edu) about them.

Some packages are distributed only as generic source code (such as ANSI C source code). I have judged that they will be compilable mostly on Unix systems, unless specific support is provided by the author for compilers on PC's, or Macintosh systems. So I have listed them under "Unix" only. If you feel comfortable running the compiler on a non-Unix system you might also want to look into the Unix listings to see which packages are available as generic source code. (Note, though, that Mac OS X is actually a kind of Unix, so that it can also compile and run most generic Unix applications, and also that there are now implementations of the Gnu C++ compiler on Windows systems such as CygWin and MinGW that enable generic C source code to be compiled there using only Makefiles). For the purposes of this listing, Linux is Unix, which is true in all major functional senses, if not in the legal sense.

Programs in the Java language are listed here under Unix, Windows, and Macintosh, as Java is widely available on these systems. Programs requiring interpreted languages such as Perl, Tcl/Tk, Python and R are listed here under Unix but would be runnable on other systems if you had the appropriate language loaded.

	Systems on which they work
	Unix (or generic source code only)	DOS (and in a Command Tool "DOS box" in Windows)	Windows	Mac OS or Mac OS X
Method
General-purpose	PHYLIP PAUP* Phylo_win ARB PAL Mesquite BIRCH Bosque EMBOSS	PHYLIP PAUP* MEGA Bosque	PHYLIP PAUP* DAMBE PAL Bionumerics Mesquite Phylo_win NimbleTree PaupUp Bosque	PHYLIP PAUP* PAL Mesquite Phylo_win
Parsimony	PHYLIP PAUP* gmaes Phylo_win sog LVB TAAR ARB MALIGN POY TCS GAPars PAUPRat Mesquite TNT FootPrinter BPAnalysis Parsimov Notung galaxie BIRCH CRANN IDEA PSODA PRAP SeqState Bosque PhyloNet EMBOSS	PHYLIP PAUP* Hennig86 MEGA RA Nona MALIGN POY Gambit LVB PAUPRat Network BPAnalysis	PHYLIP PAUP* GeneTree DAMBE Nona TNT Gelcompar II Bionumerics TCS Mesquite Phylo_win PAST Network Simplot NimbleTree PaupUp Notung CRANN PSODA PRAP SeqState Bosque PhyloNet	PHYLIP PAUP* CAFCA GeneTree TCS LVB PAUPRat Mesquite Phylo_win TNT Notung CRANN PSODA PRAP SeqState PhyloNet
	Unix (or generic source code only)	DOS (and in a Command Tool "DOS box" in Windows)	Windows	Mac OS or Mac OS X
Distance matrix	PHYLIP PAUP* ODEN GCG Wisconsin Package SeqPup Lintre POPTREE gmaes TreePack Phylo_win BIONJ ARB Darwin sendbs nneighbor weighbor QR2 MINSPNET PAL Arlequin vCEBL HY-PHY Vanilla qclust TCS Populations T-REX SplitsTree FastME APE QuickTree ProfDist STC CBCAnalyzer galaxie Geneious BIRCH SEMPHY FASTML Rate4Site SWORDS IDEA Bosque GAME Bioinformatics Toolbox EMBOSS	PHYLIP PAUP* MEGA TREECON DISPAN RESTSITE NTSYSpc METREE Hadtree PHYLTEST POPTREE BIONJ Lintre T-REX sendbs weighbor Gambit qclust SYN-TAX FastME Discovery Studio Gene	PHYLIP PAUP* TREECON GDA SeqPup WET Fingerprinting II Informatix Software BIONJ TFPGA DAMBE DNASIS PAL Arlequin vCEBL HY-PHY Vanilla Gelcompar II Bionumerics TCS Populations T-REX Winboot SYN-TAX PTP qclust Phylo_win SplitsTree Simplot ProfDist START STC NimbleTree CBCAnalyzer PaupUp Geneious SEMPHY FASTML Rate4Site SWORDS FAMD Bosque GAME TreeFit	PHYLIP PAUP* MacT TreeTree SeqPup Fingerprinting II Informatix Software T-REX weighbor PAL Arlequin vCEBL HY-PHY Vanilla TCS SYN-TAX qclust Phylo_win SplitsTree MacVector ProfDist Geneious SEMPHY SWORDS GAME
	Unix (or generic source code only)	DOS (and in a Command Tool "DOS box" in Windows)	Windows	Mac OS or Mac OS X
Compute distances	PHYLIP PAUP* RSVP Microsat OSA TREE-PUZZLE GCG Wisconsin Package AMP GCUA DERANGE2 DISTANCE Darwin sendbs PAML puzzleboot PAL Arlequin Vanilla qclust Populations Phylo_win MSA APE T-REX LDDist GeneContent CBCAnalyzer SEMPHY SWORDS rRNA phylogeny GAME Bioinformatics Toolbox analysis EMBOSS	PHYLIP PAUP* Microsat DIPLOMO DISPAN RESTSITE NTSYSpc TREE-PUZZLE Hadtree REAP MVSP sendbs K2WuLi qclust FSTAT SYN-TAX MSA DIVAGE Genepop	PHYLIP PAUP* TREECON GDA WET TFPGA MVSP RSTCALC Genetix Arlequin DAMBE DnaSP PAML PAL Vanilla Gelcompar II Bionumerics Populations Winboot SYN-TAX qclust Phylo_win Phyltools MSA YCDMA NSA T-REX START Swaap Swaap PH GeneContent SPAGeDi CBCAnalyzer PaupUp SEMPHY SWORDS rRNA phylogeny FAMD GAME TreeFit	PHYLIP PAUP* RAPDistance Microsat TREE-PUZZLE GCUA POPGENE GeneStrut PAML PAL Arlequin Vanilla SYN-TAX qclust Phylo_win MSA T-REX SEMPHY SWORDS GAME GenoDive
	Unix (or generic source code only)	DOS (and in a Command Tool "DOS box" in Windows)	Windows	Mac OS or Mac OS X
Maximum likelihood and Bayesian methods	PHYLIP PAUP* fastDNAml MOLPHY PAML SplitsTree PLATO TREE-PUZZLE SeqPup Phylo_win PASSML ARB Darwin BAMBE TreeCons VeryfastDNAml PAL dnarates TrExMl HY-PHY Vanilla rate-evolution RevDNArates fastDNAmlrev MrBayes PAUPRat EDIBLE Mesquite Modeltest Treefinder MetaPIGA RAXML PHASE PHYML BEAST r8s-bootstrap MrBayes tree scanners MrMrMTgui MrModeltest BootPHYML p4 Porn* Rhino IM ProtTest ModelGenerator MrAIC Modelfit IQPNNI PARAT ALIFRITZ PhyNav DPRML MultiPhyl DT-ModSel BAli-Phy CoMET BIRCH Mac5 BayesPhylogenies Kakusan2 GARLI PHYSIG MrBayesPlugin SEMPHY FASTML Rate4Site McRate PhyloBayes BEST EREM IDEA PROCOV DART PhyloCoCo AMBIORE PRAP SeqState Leaphy NHML SLR rRNA phylogeny Bosque Concaterpillar PHYLLAB Codeml3X CodeAxe EMBOSS	PHYLIP PAUP* TREE-PUZZLE Hadtree PAUPRat SplitsTree	PHYLIP PAUP* MOLPHY SeqPup Spectrum DAMBE PAML PAL Modeltest HY-PHY Vanilla Bionumerics MrBayes EDIBLE Mesquite PTP Phylo_win Treefinder MetaPIGA PHASE PHYML BEAST MrMrMTgui MrModeltest Spectronet IM ProtTest ModelGenerator Simplot MDIV IQPNNI DPRML MultiPhyl NimbleTree PaupUp SSA BAli-Phy CoMET Mac5 BayesPhylogenies Kakusan2 GARLI MrBayesPlugin SEMPHY FASTML Rate4Site aLRT McRate BEST EREM PRAP SeqState Leaphy SLR rRNA phylogeny Bosque	PHYLIP PAUP* fastDNAml PAML Spectrum SplitsTree PLATO TREE-PUZZLE SeqPup Modeltest PAL HY-PHY Vanilla MrBayes PAUPRat Mesquite Phylo_win Treefinder MetaPIGA PHYML BEAST MrModeltest BootPHYML SIMMAP Rhino ProtTest ModelGenerator IQPNNI DPRML MultiPhyl BAli-Phy CoMET Mac5 BayesPhylogenies Kakusan2 GARLI MrBayesPlugin SEMPHY aLRT BEST PhyloCoCo PRAP SeqState SLR
	Unix (or generic source code only)	DOS (and in a Command Tool "DOS box" in Windows)	Windows	Mac OS or Mac OS X
Quartets methods	TREE-PUZZLE SplitsTree Darwin PhyloQuart Willson quartets programs IQPNNI STC Quartet Suite LEVEL2 Bosque	TREE-PUZZLE PHYLTEST GEOMETRY PICA Gambit	SplitsTree IQPNNI STC Quartet Suite LEVEL2 Bosque	TREE-PUZZLE SplitsTree Willson quartets programs IQPNNI Quartet Suite LEVEL2
Artificial Intelligence and Genetic Algorithms	GAPars MetaPIGA GARLI		PTP MetaPIGA GARLI	MetaPIGA GARLI
Invariants	PHYLIP PAUP* BIRCH EMBOSS	PHYLIP PAUP*	PHYLIP PAUP* PaupUp	PHYLIP PAUP*
Interactive tree rearrangement	PHYLIP ARB UO Mavric EDIBLE Mesquite Treefinder TreeView TreeJuxtaposer Notung TreeMaker TreeDyn BIRCH Dendroscope Forest Phylocom TreeToy Bioinformatics Toolbox Phyutility EMBOSS	PHYLIP PDAP Phylo_win	PHYLIP WINCLADA TreeExplorer T-REX EDIBLE Mesquite Treefinder TreeView TreeJuxtaposer TreeMe ArboDraw Notung TreeMaker TreeDyn SimpleClade TreeIllustrator Dendroscope Phylocom TreeToy	MacClade PHYLIP TreeEdit TreeThief RadCon T-REX Mesquite Treefinder TreeView TreeJuxtaposer Notung TreeMaker TreeDyn TreeIllustrator Dendroscope Phylocom TreeToy
Recombination and hybridization	PLATO TOPALi reticulate RecPars partimatrix LARD TCS PPH PIST IM Likewind DualBrothers cBrother TreeMos EEEP HGT PhyloNet EvolSimulator Concaterpillar NEPAL	Network	TCS SiScan Network PPH T-REX Spectronet IM Simplot START DualBrothers TreeMos TOPALi EEEP PhyloNet	PLATO LARD TCS PPH T-REX PIST DualBrothers TreeMos TOPALi PhyloNet
	Unix (or generic source code only)	DOS (and in a Command Tool "DOS box" in Windows)	Windows	Mac OS or Mac OS X
Bootstrapping and other measures of support	PHYLIP PAUP* OSA Lintre sog POPTREE TreeCons BAMBE puzzleboot TrEXMl PAL PHYCON CONSEL Populations MrBayes LVB EDIBLE CodonBootstrap Modeltest Mesquite Phylo_win Treefinder RAXML PHASE PHYML BEAST r8s-bootstrap MrBayes tree scanners MrMrMTgui MrModeltest BootPHYML ProtTest ModelGenerator MCS ELW MultiPhyl GHOSTS Geneious BIRCH scaleboot PhyloBayes SWORDS CTree PRAP bootscore PhyloNet PHYLLAB Phyutility EMBOSS	PHYLIP PAUP* Random Cladistics DISPAN PHYLTEST POPTREE PICA TAXEQ3 GambiT MEGA CONSEL LVB Porn* Discovery Studio Gene	PHYLIP PAUP* DAMBE PAL MEGA Gelcompar II Bionumerics Populations Modeltest MrBayes EDIBLE Winboot Mesquite Phylo_win PAST Treefinder Phyltools PHASE PHYML BEAST T-REX MrMrMTgui MrModeltest ProtTest ModelGenerator Simplot MCS MultiPhyl PaupUp Geneious aLRT SWORDS CTree PRAP FAMD PhyloNet	PHYLIP PAUP* AutoDecay TreeRot DNA Stacks TreeTree Modeltest PAL MrBayes LVB Mesquite Phylo_win Treefinder PHYML BEAST T-REX MrModeltest BootPHYML ProtTest ModelGenerator MCS Permute! MultiPhyl Geneious aLRT SWORDS CTree PRAP PhyloNet
	Unix (or generic source code only)	DOS (and in a Command Tool "DOS box" in Windows)	Windows	Mac OS or Mac OS X
Compatibility	COMPROB PHYLIP reticulate partimatrix CLINCH PPH BIRCH EMBOSS	PHYLIP PICA CLINCH	PHYLIP PPH Spectronet	PHYLIP PPH
Consensus trees, subtrees, supertrees, and distances between trees	PHYLIP PAUP* Mesquite Treefinder Robinson and Foulds distance Clann PhyNav Supertree scripts Supertree BIRCH HeuristicMRF2 TopD/fMts Quartet Suite Rainbow PhySIC EEEP PhyloSort bootscore PhyloNet Phyutility EMBOSS	NTSYSpc PHYLIP PAUP* REDCON TAXEQ3 MEGA TreeCons Robinson and Foulds distance	COMPONENT TREEMAP PHYLIP PAUP* MEGA Mesquite PAST Treefinder Clann PaupUp Quartet Suite Rainbow EEEP PhyloSort FAMD PhyloNet	PHYLIP PAUP* TREEMAP COMPONENT RadCon Mesquite Treefinder Robinson and Foulds distance Clann Supertree Quartet Suite Rainbow PhySIC PhyloSort PhyloNet
Tree-based Alignment	TreeAlign ClustalW MALIGN TAAR Ctree POY FootPrinter ALIFRITZ T-Coffee BAli-Phy galaxie Geneious BIRCH MAFFT SATCHMO DART MUSCLE Bosque EMBOSS	ClustalW MALIGN POY	GeneDoc Ctree DAMBE DNASIS ArboDraw BAli-Phy Geneious MAFFT SATCHMO MUSCLE Bosque	ClustalW ALIGN BAli-Phy Geneious MAFFT MUSCLE
	Unix (or generic source code only)	DOS (and in a Command Tool "DOS box" in Windows)	Windows	Mac OS or Mac OS X
Gene duplication and genomic analysis	FORESTER DERANGE2 BPAnalysis GeneContent Notung TopD/fMts DTscore DART gtp EvolSimulator DTdraw Tree Tracker	BPAnalysis	Mgenome GeneContent Notung DTscore	Notung
Biogeographic or host-parasite	GEODIS Tarzan ParaFit Phylocom AxParafit	DIVA TreeFitter	COMPONENT TREEMAP GEODIS MDIV ParaFit Phylocom AxParafit	TREEMAP COMPONENT DIVA TreeFitter GEODIS ParaFit Phylocom AxParafit
Comparative method	PHYLIP COMPARE ANCML RIND Mesquite APE Jevtrace TreeScan PHYLOGR TreeSAAP Parsimov DIVERGE IDC OUCH BIRCH BayesTraits PHYSIG Cactus-Pie Phylocom pcca EMBOSS	PHYLIP COMPARE CMAP CoSta PDAP ACAP ANCML TreeScan	PHYLIP Phylogenetic Independence Mesquite Jevtrace PHYLOGR TreeSAAP DIVERGE IDC BayesTraits Phylocom pcca	PHYLIP MacClade CAIC MacroCAIC COMPARE Mesquite Jevtrace SIMMAP TreeScan PHYLOGR TreeSAAP Permute! BayesTraits Phylocom pcca
	Unix (or generic source code only)	DOS (and in a Command Tool "DOS box" in Windows)	Windows	Mac OS or Mac OS X
Simulation	Bi-De TheSiminator Seq-Gen P/Treevolve PSeq-Gen COMPARE ROSE PAML PAL Vanilla EDIBLE Mesquite Treefinder Hetero Phyl-O-Gen apTreeshape Simprot EREM indel-Seq-Gen DAWG EvolveAGene3 EvolSimulator	COMPARE	COMPONENT COMPARE PAML ProSeq PAL Vanilla EDIBLE Mesquite Treefinder Hetero Phyl-O-Gen MESA Simprot EREM EvolveAGene3	Bi-De TheSiminator Seq-Gen P/Treevolve PSeq-Gen COMPONENT PAML ProSeq COMPARE PAL Vanilla MacClade Mesquite Treefinder Hetero Phyl-O-Gen MESA SGRunner indel-Seq-Gen EvolveAGene3
Shapes of trees	Genie PAL Vanilla BRANCHLENGTH APE Tracer SymmeTREE apTreeshape TreeStat CTree		Genie PAL Vanilla Tracer SymmeTREE MESA TreeStat CTree	MacroCAIC Genie PAL Vanilla RadCon Tracer SymmeTREE MESA TreeStat CTree
	Unix (or generic source code only)	DOS (and in a Command Tool "DOS box" in Windows)	Windows	Mac OS or Mac OS X
Clocks, dating, and stratigraphy	PHYLIP QDate Diversi PAML TipDate RRTree vCEBL HY-PHY PAL rate-evolution BRANCHLENGTH r8s Modeltest Treefinder APE BEAST MrMTgui MrModeltest SymmeTREE Porn* Rhino GHOSTS Multidivtime CodonRates BIRCH Brownie PATHd8 McRate PhyloBayes Cactus-Pie NHML MULTIDIVTIME HELPER EMBOSS	PHYLIP MEGA K2WuLi	PHYLIP PAML RRTree TipDate vCEBL HY-PHY MEGA PAL Modeltest PAST Treefinder QDate Diversi BEAST MrMTgui MrModeltest SymmeTREE Multidivtime CodonRates Brownie PATHd8 McRate GRate TreeFit	PHYLIP QDate Modeltest PAML TipDate RRTree vCEBL TreeEdit HY-PHY PAL r8s Modeltest Treefinder BEAST MrModeltest SymmeTREE Rhino Cadence Brownie PATHd8 Ultrametric Check
Model selection	Modeltest MrMTgui MrModeltest Porn* ModelGenerator ProtTest MrAIC Modelfit DT-ModSel BayesTraits Kakusan2 DART Concaterpillar		Modeltest MrMTgui MrModeltest ModelGenerator ProtTest BayesTraits Kakusan2	Modeltest MrModeltest ModelGenerator ProtTest BayesTraits Kakusan2 MAPPS
Description or Prediction of data	EDIBLE RIND Jevtrace TreeSAAP DIVERGE FASTML RPT	TreeDis	EDIBLE Jevtrace TreeSAAP DIVERGE MESA FASTML	CONSERVE Jevtrace SIMMAP TreeSAAP MESA
	Unix (or generic source code only)	DOS (and in a Command Tool "DOS box" in Windows)	Windows	Mac OS or Mac OS X
Tree drawing	PHYLIP PAUP* TreeTool Phylodendron ARB NJplot unrooted Mavric FORESTER Mesquite APE TreeView TreeJuxtaposer TreeSetViz TreeGraph Notung TreeDyn DigTree Geneious BIRCH Paloverde FigTree HyperTree Dendroscope CTree RPT TreeToy TreeSnatcher DTdraw Bioinformatics Toolbox PHYLAB EMBOSS	PHYLIP MEGA PAUP*	PHYLIP PAUP* TreeView Phylodendron NJplot unrooted DAMBE TreeExplorer Bionumerics FORESTER MEGA T-REX Mesquite TreeJuxtaposer Spectronet TreeSetViz TreeMe TreeGraph ArboDraw PaupUp Notung TreeDyn DigTree Geneious MrEnt FigTree TreeIllustrator HyperTree GeoPhyloBuilder Dendroscope CTree TreeToy TreeSnatcher	PHYLIP PAUP* Tree Draw Deck NJplot TreeView DendroMaker Phylodendron unrooted TREECON TreeThief FORESTER MacClade T-REX Mesquite TreeJuxtaposer TreeSetViz Notung TreeDyn Geneious Paloverde FigTree TreeIllustrator HyperTree Dendroscope CTree TreeToy TreeSnatcher
Data management or job submission	GDE SeqPup ARB Singapore PHYLIP web interface PHYCON DPRML galaxie Geneious BIRCH TOPALi IDEA MBEToolbox PISE Bosque EMBOSS	Random Cladistics MUST 2000	SeqPup BioEdit Singapore PHYLIP web interface Bionumerics W2H Phyledit GeneStudio Pro Simplot NimbleTree DPRML Geneious TOPALi MBEToolbox Bosque	DNA Stacks SeqPup Singapore PHYLIP web interface DPRML Geneious TOPALi
Teaching	Phylap Dnatree		Phylap Dnatree SimpleClade	Phylogenetic Investigator Phylap Dnatree

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