This table lists packages by method (down the side of the table) cross-referenced with systems on which the programs work (across the top). 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 (joe@genetics.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, Macs or VMS 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 there are now implementations of the Gnu C++ compiler on Windows systems such as CygWin and Mingw32 that enable generic C source code to be compiled there using only Makefiles).

Programs in the Java language are listed here under Unix, Windows, and Macintosh, as Java is widely available on these systems.

	System on which they work
	Unix (or generic source code only)	DOS (and in a Windows "DOS box")	Windows	Mac or PowerMac	VMS or OpenVMS
Method
General-purpose	PHYLIP PAUP* Zharkikh Fitch programs Phylo_win ARB	PHYLIP PAUP* MEGA VOSTORG Fitch programs	PHYLIP PAUP* DAMBE	PHYLIP PAUP*	PHYLIP Phylo_win
Parsimony	PHYLIP PAUP* PHYSYS Fitch programs gmaes Phylo_win sog LVB TAAR ARB MALIGN POY	PHYLIP PAUP* Hennig86 MEGA RA Pee-Wee/Noname PHYSYS TurboTree Freqpars Fitch programs MALIGN POY	PHYLIP PAUP* Tree Gardener GeneTree DAMBE LVB	PHYLIP PAUP* CAFCA GeneTree	PHYLIP PAUP* Phylo_win
Distance matrix	PHYLIP PAUP* ODEN Fitch programs SINCAIDEN GCG SeqPup Lintre njbafd gmaes TreePack GTREE/ Phylo_win BIONJ qclust ARB BIOSYS-2 Darwin sendbs nnneighbor weighbor QR2	PHYLIP PAUP* MEGA Fitch programs ABLE TREECON DISPAN RESTSITE NTSYSpc METREE Hadtree PHYLTEST njbafd BIONJ qclust Lintre BIOSYS-2 T-REX sendbs weighbor	PHYLIP PAUP* TREECON GDA SeqPup WET Molecular  Analyst BIONJ TFPGA DAMBE	PHYLIP PAUP* MacT TreeTree SeqPup Molecular  Analyst T-REX weighbor	PHYLIP PAUP* GCG Phylo_win
Compute distances	PHYLIP PAUP* MARKOV RSVP Microsat OSA PUZZLE GCG AMP DISTREE GCUA DERANGE2 qclust BIOSYS-2 RAPD-PCR DISTANCE Darwin sendbs PAML puzzleboot	PHYLIP PAUP* Microsat DIPLOMO DISPAN RESTSITE NTSYSpc PUZZLE Hadtree DISTREE qclust REAP MVSP BIOSYS-2 RAPD-PCR sendbs K2WuLi	PHYLIP PAUP* TREECON GDA WET TFPGA MVSP RSTCALC Genetix Arlequin DAMBE DnaSP PAML	PHYLIP PAUP* RAPDistance Microsat PUZZLE GCUA POPGENE GeneStrut PAML MATRIX	PHYLIP PAUP* MARKOV Microsat PUZZLE GCG
	Unix (or generic source code only)	DOS (or in a Windows "DOS box")	Windows	Mac or PowerMac	VMS or OpenVMS
Maximum likelihood	PHYLIP PAUP* fastDNAml MOLPHY PAML SplitsTree PLATO SPOT PUZZLE SeqPup Phylo_win ARB Darwin BAMBE TreeCons VeryfastDNAml	PHYLIP PAUP* SPOT PUZZLE Hadtree	PHYLIP PAUP* MOLPHY SeqPup Spectrum DAMBE PAML	PHYLIP PAUP* fastDNAml PAML Spectrum SplitsTree PLATO SPOT PUZZLE SeqPup Modeltest	PHYLIP PAUP* fastDNAml PUZZLE Phylo_win
Quartets methods	PUZZLE STATGEOM SplitsTree Darwin PhyloQuart Willson quartets  programs	PUZZLE PHYLTEST GEOMETRY PICA95		PUZZLE SplitsTree Willson quartets  programs	PUZZLE
Artificial Intelligence	SOTA
Invariants	PHYLIP PAUP*	PHYLIP PAUP* Evomony	PHYLIP PAUP*	PHYLIP PAUP*	PHYLIP PAUP*
Tree rearrangement	PHYLIP ARB	PHYLIP ClaDOS PDAP	PHYLIP	MacClade PHYLIP	PHYLIP
Recombination	PLATO Bootscanning  Package TOPAL reticulate RecPars partimatrix LARD	homoplasy test		PLATO LARD
Bootstrapping etc.	PHYLIP PAUP* Zharkikh PARBOOT OSA Lintre sog njbafd BIOSYS-2 RAPD-PCR TreeCons BAMBE puzzleboot	PHYLIP PAUP* ABLE Random Cladistics DISPAN PHYLTEST njbafd PICA95 TAXEQ2 BIOSYS-2 RAPD-PCR	PHYLIP PAUP* DAMBE	PHYLIP PAUP* AutoDecay TreeRot RASA DNA Stacks TreeTree	PHYLIP PAUP*
Compatibility	COMPROB PHYLIP reticulate partimatrix	CLINCH PHYLIP PICA95	PHYLIP	PHYLIP	PHYLIP
Consensus trees and distances between trees	PHYLIP PAUP*	NTSYSpc PHYLIP PAUP* REDCON TAXEQ2 TreeCons	COMPONENT TREEMAP PHYLIP PAUP*	PHYLIP PAUP* TREEMAP COMPONENT	PHYLIP
Tree-based Alignment	TreeAlign ClustalW MALIGN TAAR Ctree POY	ClustalW MALIGN POY	GeneDoc Ctree DAMBE	ClustalW ALIGN	ClustalW TreeAlign GCG
	Unix (or generic source code only)	DOS (or in a Windows "DOS box")	Windows	Mac or PowerMac	VMS or OpenVMS
Biogeographic or host-parasite			COMPONENT TREEMAP	TREEMAP COMPONENT
Comparative method	PHYLIP COMPARE ANCML RIND	PHYLIP COMPARE CMAP CoSta PDAP ACAP ANCML	PHYLIP COMPARE	PHYLIP MacClade CAIC PA	PHYLIP
Simulation	Bi-De SEQEVOLVE TheSiminator Seq-Gen P/Treevolve PSeq-Gen COMPARE ROSE PAML	COMPARE	COMPONENT COMPARE PAML	Bi-De SEQEVOLVE TheSiminator Seq-Gen P/Treevolve PSeq-Gen COMPONENT PAML
Shapes of trees				End-Epi
Clocks, dating, and stratigraphy	QDate DIVERSI PAML	DIVERSI K2WuLi	PAML	StratCon QDate Modeltest PAML
Prediction of data				CONSERVE
Tree drawing	PHYLIP PAUP* TreeTool Fitch programs Phylodendron ARB NJplot unrooted	PHYLIP PAUP*	PHYLIP PAUP* TreeView Phylodendron NJplot unrooted DAMBE	PHYLIP PAUP* Tree Draw Deck NJplot TreeView DendroMaker Phylodendron unrooted	PHYLIP PAUP*
Data management or job submission	PARBOOT GDE SeqPup ARB	Random Cladistics MUST Tonex	Tree Gardener SeqPup Tonex	DNA Stacks SeqPup
Teaching				Phylogenetic  Investigator Systack

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