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 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.

A column for multiplatform environments including Java, R, Perl, Python, MATLAB, and Tcl/Tk is in the process of being added. At the moment many packages working in these languages are included in the Unix or generic Source Code column. Please keep this in mind.

	Systems on which they work
	Unix (or generic source code only)	Multiplatform interpreters (Java, R, Perl, Python, Tcl/Tk, MATLAB)	Linux executables	Windows	Mac OS X or Mac OS	DOS (and in a Command Prompt "DOS box" in Windows)
Method
General-purpose	PHYLIP Phylo_win ARB PAL Mesquite BIRCH EMBOSS Bio++ ETE SeaView	Java: PAL Mesquite BIRCH Python: ETE DendroPy BIRCH Crux R: phangorn	PHYLIP PAUP* Bio++ Phylo_win SeaView ARB Bosque	PHYLIP PAUP* MEGA DAMBE Bionumerics Phylo_win NimbleTree PaupUp Bosque Bio++ ETE SeaView	PHYLIP PAUP* MEGA Phylo_win Bio++ Bosque ETE SeaView	PHYLIP PAUP*
Parsimony	PHYLIP gmaes Phylo_win sog LVB ARB MALIGN POY GAPars Mesquite FootPrinter BPAnalysis BIRCH PSODA EMBOSS phangorn Murka Freqpars SeaView	Java: PRAP Mesquite SeqState TCS IDEA PhyloNet Notung BIRCH Perl: Parsimov IDEA Python: BIRCH	PHYLIP PAUP* PAUPRat TNT Murka CRANN LVB PSODA IDEA Phylo_win MALIGN POY SeaView ARB Bosque	PHYLIP PAUP* GeneTree DAMBE Nona TNT Gelcompar II Bionumerics Phylo_win MALIGN POY PAST Network Simplot NimbleTree PaupUp CRANN PSODA Bosque Murka SeaView PAUPRat	PHYLIP PAUP* GeneTree CAFCA LVB Phylo_win POY TNT CRANN PSODA Bosque SeaView	PHYLIP PAUP* Hennig86 MEGA RA Nona Gambit LVB Network BPAnalysis PAUPRat
	Unix (or generic source code only)	Multiplatform interpreters (Java, R, Perl, Python, Tcl/Tk, MATLAB)	Linux executables	Windows	Mac OS X or Mac OS	DOS (and in a Command Prompt "DOS box" in Windows)
Distance matrix	PHYLIP ODEN SeqPup Lintre POPTREE2 gmaes TreePack Phylo_win BIONJ ARB sendbs nneighbor weighbor QR2 MINSPNET PAL Arlequin HY-PHY Vanilla qclust Populations T-REX QuickTree ProfDist SplitsTree CBCAnalyzer BIRCH SEMPHY FASTML Rate4Site SWORDS IDEA GAME EMBOSS phangorn Mesquite Bio++ UGENE NINJA SeaView Ancestor ANC-GENE Bn-Bs	Java: PAL Vanilla Mesquite TCS NINJA qclust PEBBLE IDEA SplitsTree BIRCH SeqPup Python: BIRCH Crux R: APE MATLAB: Bioinformatics Toolbox	PHYLIP PAUP* Bio++ FastME BIONJ Darwin weighbor STC SWORDS SEMPHY Phylo_win SplitsTree SeaView SeqPup Bosque UGENE	PHYLIP PAUP* TREECON GDA SeqPup BIONJ TFPGA DAMBE DNASIS Arlequin HY-PHY Gelcompar II Bionumerics Populations T-REX Winboot SYN-TAX PTP NTSYSpc Phylo_win SplitsTree Simplot ProfDist START STC NimbleTree CBCAnalyzer PaupUp SEMPHY FASTML Rate4Site SWORDS FAMD Bosque IDEA GAME TreeFit FastME DENDRON PC-ORD Bio++ UGENE POPTREE2 SeaView TIMER	PHYLIP PAUP* MacT SeqPup T-REX weighbor Arlequin HY-PHY SYN-TAX Phylo_win SplitsTree MacVector ProfDist SEMPHY SWORDS GAME FastME Bio++ Bosque UGENE SeaView	PHYLIP PAUP* MEGA TREECON DISPAN RESTSITE METREE PHYLTEST POPTREE2 BIONJ Lintre T-REX sendbs weighbor Gambit qclust SYN-TAX Statio Ancestor ANC-GENE Bn-Bs
	Unix (or generic source code only)	Multiplatform interpreters (Java, R, Perl, Python, Tcl/Tk, MATLAB)	Linux executables	Windows	Mac OS X or Mac OS	DOS (and in a Command Prompt "DOS box" in Windows)
Compute distances	PHYLIP RSVP Microsat OSA TREE-PUZZLE DERANGE2 DISTANCE sendbs PAML puzzleboot PAL Arlequin Vanilla qclust Populations Phylo_win MSA T-REX LDDist CBCAnalyzer SEMPHY SWORDS rRNA phylogeny GAME analysis EMBOSS Murka Bio++ UGENE POPTREE2 DISTREE SeaView Bn-Bs HON-new	Java: PAL Vanilla Perl: LDDist Python: Crux R: APE Bioinformatics Toolbox	PHYLIP PAUP* Bio++ Murka GCUA GAME Darwin SWORDS SEMPHY Phylo_win TREE-PUZZLE SeaView MULTICOMP MSA rRNA phylogeny UGENE HON-new	PHYLIP PAUP* TREECON GDA TFPGA MVSP RSTCALC Genetix Arlequin DAMBE DnaSP PAML Gelcompar II Bionumerics Populations Winboot SYN-TAX qclust Phylo_win TREE-PUZZLE Phyltools MSA YCDMA NSA T-REX START Swaap Swaap PH SPAGeDi CBCAnalyzer PaupUp SEMPHY SWORDS rRNA phylogeny FAMD GAME TreeFit Murka Bio++ UGENE POPTREE2 SeaView	PHYLIP PAUP* RAPDistance Microsat TREE-PUZZLE GCUA POPGENE PAML Arlequin SYN-TAX qclust Phylo_win MSA T-REX SEMPHY SWORDS GAME GenoDive Bio++ UGENE SeaView	PHYLIP PAUP* Microsat DIPLOMO DISPAN RESTSITE NTSYSpc TREE-PUZZLE REAP MVSP sendbs qclust FSTAT SYN-TAX MSA DIVAGE Genepop POPTREE2 DISTREE Bn-Bs
	Unix (or generic source code only)	Multiplatform interpreters (Java, R, Perl, Python, Tcl/Tk, MATLAB)	Linux executables	Windows	Mac OS X or Mac OS	DOS (and in a Command Prompt "DOS box" in Windows)
Maximum likelihood methods	PHYLIP fastDNAml MOLPHY PAML TREE-PUZZLE SeqPup Phylo_win PASSML PARBOOT ARB TipDate PAL dnarates HY-PHY Vanilla rate-evolution SplitsTree RevDNArates fastDNAmlrev PLATO EDIBLE Mesquite Modeltest MetaPIGA RAXML MrMrMTgui MrModeltest P4 ProtTest ModelGenerator IQPNNI PARAT ALIFRITZ SSA BIRCH Mac5 GARLI SEMPHY FASTML Rate4Site McRate EREM IDEA PROCOV DART NHML SLR rRNA phylogeny Codeml3X CodeAxe EMBOSS phangorn tracer Bio++ FastTree nhPhyML PhyML-Multi raxmlGUI MixtureTree SeaView GZ-Gamma	Java: PRAP PAL Vanilla Mesquite SeqState DPRML MultiPhyl IDEA Treefinder PhyloCoCo ProtTest SplitsTree CoMET BIRCH SeqPup Segminator Perl: r8s-bootstrap BootPHYML PARBOOT Modelfit MrAIC DT-ModSel Kakusan2 burntrees bms_runner Python: Porn* Concaterpillar p4 BIRCH Crux MATLAB: PHYLLAB PHYSIG	PHYLIP PAUP* PAUPRat fastDNAml Bio++ Darwin IDEA Segminator SLR PHYML nhPhyML PhyML-Multi SSA SEMPHY Leaphy PhyNav MixtureTree FastTree aLRT Phylo_win TREE-PUZZLE SplitsTree IQPNNI ALIFRITZ SeaView SeqPup rRNA phylogeny Bosque NHML	PHYLIP PAUP* MOLPHY SeqPup Spectrum SplitsTree DAMBE PAML Modeltest HY-PHY Bionumerics EDIBLE PTP Phylo_win TREE-PUZZLE MetaPIGA PHYML MrMrMTgui MrModeltest Spectronet Simplot IQPNNI NimbleTree PaupUp SSA Mac5 GARLI SEMPHY FASTML Rate4Site aLRT McRate P4 EREM Leaphy SLR rRNA phylogeny Bosque tracer Bio++ FastTree Segminator raxmlGUI SeaView	PHYLIP PAUP* fastDNAml PAML Spectrum SplitsTree TREE-PUZZLE SeqPup PLATO Modeltest HY-PHY Phylo_win TipDate MetaPIGA PHYML MrModeltest P4 SIMMAP IQPNNI Mac5 GARLI SEMPHY aLRT PhyloCoCo Bosque SLR tracer Segminator raxmlGUI SeaView PAUPRat	PHYLIP PAUP* TREE-PUZZLE GZ-Gamma PAUPRat
	Unix (or generic source code only)	Multiplatform interpreters (Java, R, Perl, Python, Tcl/Tk, MATLAB)	Linux executables	Windows	Mac OS X or Mac OS	DOS (and in a Command Prompt "DOS box" in Windows)
Bayesian methods	BAMBE MrBayes PHASE IMa2 AMBIORE BAli-Phy P4 PhyloBayes BEST tracer ANC-GENE	Java: MrBayesPlugin MrBayes tree scanners Python: p4 Crux	PHASE BayesPhylogenies PhyloBayes BEAST	MrBayes PHASE IMa2 BAli-Phy P4 BayesPhylogenies BEST tracer	MrBayes BAli-Phy P4 BayesPhylogenies BEST	ANC-GENE
Quartets methods	TREE-PUZZLE BIRCH SplitsTree PhyloQuart Willson quartets programs IQPNNI Quartet Suite LEVEL2	Java: BIRCH SplitsTree LEVEL2 Python: BIRCH	Darwin STC TREE-PUZZLE SplitsTree IQPNNI Bosque	SplitsTree IQPNNI STC TREE-PUZZLE Quartet Suite Bosque	TREE-PUZZLE SplitsTree Willson quartets programs IQPNNI Quartet Suite Bosque	TREE-PUZZLE PHYLTEST GEOMETRY PICA Gambit
Artificial Intelligence and Genetic Algorithms	GAPars MetaPIGA GARLI			PTP MetaPIGA GARLI	MetaPIGA GARLI
Invariants	PHYLIP BIRCH EMBOSS	Java: BIRCH Python: BIRCH	PHYLIP PAUP*	PHYLIP PAUP* PaupUp	PHYLIP PAUP*	PHYLIP PAUP*
Interactive tree rearrangement	PHYLIP ARB UO EDIBLE Mesquite TreeView TreeMaker TreeDyn BIRCH Forest Phylocom TreeToy TreeJuxtaposer Toolbox Phyutility EMBOSS PhyloWidget ETE TreeGraph 2 POPTREE2 Phylo_win	Java: Mesquite Notung BIRCH TreeJuxtaposer TreeGraph 2 Dendroscope PhyloWidget TreeToy Phyutility Python: ETE p4 BIRCH Mavric Crux R: Phybase MATLAB: Bioinformatics	PHYLIP Phylo_win ARB TreeView Treefinder	PHYLIP WINCLADA TreeExplorer T-REX EDIBLE TreeView TreeMe ArboDraw TreeMaker MESA TreeDyn SimpleClade Phylocom Phybase ETE POPTREE2	MacClade PHYLIP TreeEdit TreeThief RadCon T-REX TreeView TreeMaker MESA TreeDyn Phylocom Phybase ETE POPTREE2	PHYLIP PDAP
	Unix (or generic source code only)	Multiplatform interpreters (Java, R, Perl, Python, Tcl/Tk, MATLAB)	Linux executables	Windows	Mac OS X or Mac OS	DOS (and in a Command Prompt "DOS box" in Windows)
Recombination and hybridization	TOPALi RecPars partimatrix PPH IMa2 DualBrothers cBrother EEEP HGT EvolSimulator PhyML-Multi	Java: TCS TOPALi PhyloNet Perl: PPH Likewind Python: Concaterpillar	PhyML-Multi TOPALi PPH EEEP NEPAL	Network PPH T-REX Spectronet IMa2 Simplot START DualBrothers TOPALi EEEP RDP3	PPH T-REX DualBrothers TOPALi NEPAL	Network
Bootstrapping and other measures of support	PHYLIP OSA Lintre sog POPTREE2 PARBOOT BAMBE puzzleboot PAL CONSEL Populations MrBayes LVB EDIBLE CodonBootstrap Modeltest Mesquite Phylo_win RAXML PHASE r8s-bootstrap MrMrMTgui MrModeltest ProtTest ModelGenerator ELW GHOSTS BIRCH PhyloBayes SWORDS Phyutility EMBOSS FastTree Vanilla tracer Bio++ Phybase raxmlGUI MixtureTree	Java: PRAP PAL Vanilla Mesquite CTree MultiPhyl Treefinder ProtTest ModelGenerator BEAST PhyloNet BIRCH Geneious Phyutility Perl: AutoDecay TreeRot BootPHYML PARBOOT MrBayes tree scanners burntrees Python: Porn* BIRCH R: scaleboot MATLAB: PHYLLAB	PHYLIP PAUP* Bio++ LVB SWORDS PHYML PHASE MixtureTree FastTree aLRT PhyloBayes Phylo_win	PHYLIP PAUP* DAMBE MEGA Gelcompar II Bionumerics Populations Modeltest MrBayes LVB EDIBLE Winboot Phylo_win PAST Phyltools PHASE PHYML T-REX MrMrMTgui MrModeltest Simplot PaupUp aLRT SWORDS FAMD FastTree Bionumerics tracer Bio++ Phybase POPTREE2 raxmlGUI	PHYLIP PAUP* TreeRot DNA Stacks Modeltest MrBayes LVB Phylo_win PHYML T-REX MrModeltest Permute! aLRT SWORDS tracer Bio++ Phybase raxmlGUI	PHYLIP PAUP* Random Cladistics DISPAN PHYLTEST POPTREE2 PICA TAXEQ3 Gambit MEGA CONSEL LVB
	Unix (or generic source code only)	Multiplatform interpreters (Java, R, Perl, Python, Tcl/Tk, MATLAB)	Linux executables	Windows	Mac OS X or Mac OS	DOS (and in a Command Prompt "DOS box" in Windows)
Compatibility	COMPROB PHYLIP partimatrix PPH BIRCH EMBOSS Murka	Java: BIRCH Perl: PPH Python: TIGER BIRCH	PHYLIP Murka PPH	PHYLIP PPH Spectronet Murka	PHYLIP PPH TIGER	PHYLIP PICA
Consensus trees, subtrees, supertrees, and distances between trees	PHYLIP Mesquite Robinson and Foulds distance Supertree BIRCH HeuristicMRF2 Quartet Suite Rainbow EEEP PhyloSort Phyutility EMBOSS phangorn Murka Phybase iGTP raxmlGUI	Java: Mesquite Treefinder PhyloNet TREEMAP Supertree PhyloSort BIRCH Phyutility Perl: TopD/fMts Supertree scripts Python: BIRCH Crux	PHYLIP PAUP* Murka PhyNav EEEP iGTP Clann Rainbow PhySIC	COMPONENT TREEMAP PHYLIP PAUP* MEGA NTSYSpc PAST Clann PaupUp Quartet Suite Rainbow EEEP FAMD Murka Phybase iGTP raxmlGUI	PHYLIP PAUP* TREEMAP COMPONENT RadCon Robinson and Foulds distance Clann Quartet Suite Rainbow PhySIC Phybase iGTP raxmlGUI	PHYLIP PAUP* REDCON TAXEQ3 MEGA Robinson and Foulds distance
Tree-based Alignment	TreeAlign ClustalW MALIGN Ctree POY FootPrinter ALIFRITZ T-Coffee BAli-Phy BIRCH MAFFT LOBSTER DART MUSCLE EMBOSS SeaView	Java: BIRCH Geneious SuiteMSA Perl: SuiteMSA Python: BIRCH	T-Coffee MALIGN POY ALIFRITZ MAFFT LOBSTER MUSCLE SeaView Bosque	GeneDoc Ctree DAMBE DNASIS ArboDraw BAli-Phy T-Coffee MAFFT LOBSTER MALIGN MUSCLE POY Bosque SeaView	ClustalW ALIGN BAli-Phy T-Coffee POY MAFFT MUSCLE Bosque SeaView SuiteMSA	ClustalW
	Unix (or generic source code only)	Multiplatform interpreters (Java, R, Perl, Python, Tcl/Tk, MATLAB)	Linux executables	Windows	Mac OS X or Mac OS	DOS (and in a Command Prompt "DOS box" in Windows)
Gene duplication and genomic analysis	FORESTER DERANGE2 BPAnalysis TopD/fMts DTscore DART gtp EvolSimulator Mgenome DTdraw ETE iGTP	Java: MANTiS Notung FORESTER Perl: Tree Tracker bms_runner Python: ETE	iGTP DTscore DTdraw	DTscore Mgenome ETE iGTP	ETE iGTP	BPAnalysis
Biogeographic or host-parasite	GEODIS ParaFit Phylocom AxParafit Lagrange	Java: TREEMAP Tarzan CoRe-PA Jane Python: GenGIS Lagrange R: GenGIS	AxParafit CoRe-PA	COMPONENT TREEMAP GEODIS DIVA ParaFit Phylocom AxParafit S-DIVA CoRe-PA	TREEMAP COMPONENT TreeFitter DIVA GEODIS ParaFit Phylocom AxParafit CoRe-PA	TreeFitter
Comparative method	PHYLIP COMPARE ANCML RIND Mesquite APE TreeScan TreeSAAP IDC BIRCH Phylocom EMBOSS Phybase	Java: Mesquite COMPARE TreeSAAP Jevtrace BIRCH Perl: Parsimov bms_runner Python: Cactus-Pie BIRCH R: CAIC OUCH PHYLOGR SLOUCH PHYSIG	PHYLIP Phylogenetic Independence BayesTraits pcca DIVERGE	PHYLIP Phylogenetic Independence DIVERGE IDC BayesTraits Phylocom pcca Phybase Cactus-Pie	PHYLIP MacClade MacroCAIC SIMMAP TreeScan Permute! BayesTraits Phylocom pcca Phybase	PHYLIP PDAP ANCML TreeScan
	Unix (or generic source code only)	Multiplatform interpreters (Java, R, Perl, Python, Tcl/Tk, MATLAB)	Linux executables	Windows	Mac OS X or Mac OS	DOS (and in a Command Prompt "DOS box" in Windows)
Simulation	TheSiminator Seq-Gen P/Treevolve PSeq-Gen COMPARE ROSE PAML PAL Vanilla EDIBLE Mesquite Phylogen Simprot EREM indel-Seq-Gen DAWG EvolSimulator Recodon NetRecodon	Java: PAL Vanilla Mesquite Treefinder COMPARE SuiteMSA Perl: Bio::Phylo indel-Seq-Gen EvolveAGene3 SuiteMSA Python: Crux R: apTreeshape	indel-Seq-Gen ProSeq Recodon NetRecodon	COMPONENT PAML ProSeq EDIBLE Phylogen MESA Simprot EREM EvolveAGene3 Recodon> NetRecodon	TheSiminator Seq-Gen P/Treevolve PSeq-Gen COMPONENT PAML ProSeq MacClade Phylogen MESA SGRunner indel-Seq-Gen EvolveAGene3 Recodon> NetRecodon SuiteMSA
Shapes of trees	Genie PAL Vanilla BRANCHLENGTH APE SymmeTREE apTreeshape TreeStat CTree	Java: PAL Vanilla Tracer TreeStat Perl: Bio::Phylo Python: PhyRe R: laser	Genie Perl: SymmeTREE	Genie SymmeTREE MESA TreeStat CTree PhyRe	MacroCAIC Genie RadCon SymmeTREE MESA TreeStat CTree
	Unix (or generic source code only)	Multiplatform interpreters (Java, R, Perl, Python, Tcl/Tk, MATLAB)	Linux executables	Windows	Mac OS X or Mac OS	DOS (and in a Command Prompt "DOS box" in Windows)
Clocks, dating, and stratigraphy	PHYLIP QDate PAML RRTree HY-PHY PAL rate-evolution BRANCHLENGTH Modeltest APE MrMTgui MrModeltest SymmeTREE TipDate GHOSTS Multidivtime CodonRates BIRCH PATHd8 McRate PhyloBayes NHML EMBOSS Murka	Java: PAL PEBBLE Treefinder BEAST BIRCH Python: Porn* Cactus-Pie BIRCH MATLAB: Brownie	PHYLIP Murka r8s SymmeTREE PhyloBayes PATHd8 NHML	PHYLIP PAML HY-PHY MEGA Modeltest PAST QDate MrMTgui MrModeltest SymmeTREE Multidivtime CodonRates PATHd8 McRate GRate TreeFit DAMBE Murka Cactus TIMER	PHYLIP QDate Modeltest PAML TreeEdit HY-PHY r8s Modeltest MrModeltest SymmeTREE Cadence PATHd8	PHYLIP MEGA PHYLTEST
Model selection	Modeltest MrMTgui MrModeltest ModelGenerator ProtTest DART	Java: ProtTest ModelGenerator jMODELTEST Perl: Modelfit MrAIC DT-ModSel Kakusan2 Python: Porn* Concaterpillar	BayesTraits	Modeltest MrMTgui MrModeltest BayesTraits	Modeltest MrModeltest BayesTraits MAPPS	Statio
Description or Prediction of data	EDIBLE RIND TreeSAAP FASTML RPT	Java: Jevtrace	CONSERVE DIVERGE TreeSAAP	EDIBLE CONSERVE DIVERGE MESA FASTML	CONSERVE SIMMAP MESA	TreeDis
	Unix (or generic source code only)	Multiplatform interpreters (Java, R, Perl, Python, Tcl/Tk, MATLAB)	Linux executables	Windows	Mac OS X or Mac OS	DOS (and in a Command Prompt "DOS box" in Windows)
Tree drawing	PHYLIP TreeTool Phylodendron ARB NJplot unrooted FORESTER Mesquite APE TreeView TreeJuxtaposer TreeSetViz TreeGraph 2 TreeDyn DigTree BIRCH Paloverde CTree RPT TreeToy TreeSnatcher DTdraw PHYLAB EMBOSS PhyloWidget Bio++ UGENE ETE MixtureTree SeaView Archaeopteryx	Java: Mesquite Notung BIRCH Segminator FORESTER Geneious Tree Draw Deck TreeJuxtaposer Archaeopteryx TreeSnatcher TreeSetViz TreeGraph 2 FigTree HyperTree Dendroscope PhyloWidget TreeToy SuiteMSA Perl: Bio::Phylo PhyloTreeDraw SuiteMSA Python: ETE p4 BIRCH Mavric GenGIS R: GenGIS MATLAB: Bioinformatics Toolbox	PHYLIP PAUP* Bio++ Segminator MixtureTree SeaView ARB UGENE TreeView NJplot unrooted DTdraw	PHYLIP PAUP* TreeView Phylodendron NJplot unrooted DAMBE TreeExplorer Bionumerics MEGA T-REX Spectronet TreeMe ArboDraw PaupUp TreeDyn DigTree MrEnt FigTree GeoPhyloBuilder CTree Bio++ S-DIVA UGENE ETE POPTREE2 Segminator SeaView	PHYLIP PAUP* NJplot TreeView DendroMaker Phylodendron unrooted TREECON TreeThief MacClade T-REX TreeDyn Paloverde CTree Bio++ UGENE ETE Segminator SeaView SuiteMSA	PHYLIP MEGA PAUP*
Data management or job submission	GDE SeqPup PARBOOT ARB WebPHYLIP interface BIRCH TOPALi IDEA EMBOSS PyCogent SeaView	Java: DPRML IDEA TOPALi BIRCH SeqPup Segminator SuiteMSA Perl: PARBOOT PISE Python: PyCogent BIRCH MATLAB: MBEToolbox	PyCogent IDEA Segminator TOPALi SeaView MULTICOMP MUST GDE SeqPup ARB Bosque	SeqPup BioEdit WebPHYLIP interface Bionumerics W2H Phyledit GeneStudio Pro Simplot NimbleTree TOPALi MBEToolbox Bosque PHYDIT Segminator SeaView	DNA Stacks SeqPup WebPHYLIP interface TOPALi Bosque PyCogent Segminator SeaView SuiteMSA	Random Cladistics MUST GDE
Teaching	Dnatree	Java: Phylap	Dnatree	Dnatree SimpleClade	Phylogenetic Investigator Dnatree

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