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Awesome

An open API service indexing awesome lists of open source software.

https://github.com/gvegayon/phylo-software

List of phylogenetic software. Original from Prof. Felsenstein's website https://evolution.gs.washington.edu/phylip/software.html
https://github.com/gvegayon/phylo-software

archive felsenstein genetics phylogenetics software

Last synced: 3 months ago
JSON representation

List of phylogenetic software. Original from Prof. Felsenstein's website https://evolution.gs.washington.edu/phylip/software.html

Awesome Lists containing this project

README 

          



This README.md file was generated using Pandoc applied to the website https://evolution.gs.washington.edu/phylip/software.html (Prof. Felsenstein)


  



As people can see from the dates on the most recent updates of these Phylogeny Programs pages, I have not had time to keep them up-to-date since 2012. I have now retired, which gives me more time to do research and to support online resources. So I have hopes of resuming updates, fixing links, and catching up with the field of phylogenetic inference.

I hope soon to move these software listings webpages to a Github archive, and invite others to help contribute to them and maintain them.


In the meantime, I may not be able to devote time to searching for new programs, so their authors are begged to (please!) use the submission form instead. That form will be found at the "Submitting" link below. If you are upset that your program is not included, but it's too much trouble for you to fill out the submission form, then I will not listen to you. If anyone else wants to help with this, let me know.






|                                                                             |                                                                                 |                                                                                   |                                                                                  |                                                                              |                                                                                 |                                                                                |

| :-------------------------------------------------------------------------: | :-----------------------------------------------------------------------------: | :-------------------------------------------------------------------------------: | :------------------------------------------------------------------------------: | :--------------------------------------------------------------------------: | :-----------------------------------------------------------------------------: | :----------------------------------------------------------------------------: |

| [Methods](https://evolution.gs.washington.edu/phylip/software.html#methods) | [By computer](https://evolution.gs.washington.edu/phylip/software.html#systems) | [Cross-referenced](https://evolution.gs.washington.edu/phylip/software.xref.html) | [Data types](https://evolution.gs.washington.edu/phylip/software.html#datatypes) | [Web servers](https://evolution.gs.washington.edu/phylip/software.serv.html) | [New programs](https://evolution.gs.washington.edu/phylip/software.html#recent) | [Submitting](http://evolution.gs.washington.edu/cgi-bin/software-form-new1.pl) |






|                                                                             |                                                                              |                                                                                    |                                                                              |                                                                            |                                                                       |

| :-------------------------------------------------------------------------: | :--------------------------------------------------------------------------: | :--------------------------------------------------------------------------------: | :--------------------------------------------------------------------------: | :------------------------------------------------------------------------: | :-------------------------------------------------------------------: |

| [Changes](https://evolution.gs.washington.edu/phylip/software.html#changes) | [Waiting list](https://evolution.gs.washington.edu/phylip/software.html#new) | [Other lists](https://evolution.gs.washington.edu/phylip/software.html#otherlists) | [Old programs](https://evolution.gs.washington.edu/phylip/software.old.html) | [Not listed](https://evolution.gs.washington.edu/phylip/software.not.html) | [News](https://evolution.gs.washington.edu/phylip/software.html#news) |



Here are 392 phylogeny packages and 54 [free web

servers](https://evolution.gs.washington.edu/phylip/software.serv.html#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](https://evolution.gs.washington.edu/phylip/software.html#new) 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](https://evolution.gs.washington.edu/phylip/software.serv.html#ftpservers).



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](http://evolution.gs.washington.edu/cgi-bin/software-form-new1.pl)

to submit new entries.






|                                                                                                                                                                                                                                                                                                            |

| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |

| Owing to past NSF support of these pages, I am required to note that any opinions, findings, and conclusions or recommendations expressed in this material are those of the author and do not necessarily reflect the views of the National Science Foundation (NSF supported these pages from 1995-2003). |






|                                   |

| --------------------------------- |

| **List of packages arranged ...** |



### ... [by methods available](https://evolution.gs.washington.edu/phylip/software.html#methods)



### ... [by computer systems on which they work](https://evolution.gs.washington.edu/phylip/software.html#systems)



### ... [cross-referenced by method and by computer system.](https://evolution.gs.washington.edu/phylip/software.xref.html)



### ... [by ones which analyze particular kinds of data.](https://evolution.gs.washington.edu/phylip/software.html#datatypes)



### ... [to show the most recent listings](https://evolution.gs.washington.edu/phylip/software.html#recent)



### ... [to show ones most recently changed](https://evolution.gs.washington.edu/phylip/software.html#changes)



### [Phylogeny programs formerly listed here](https://evolution.gs.washington.edu/phylip/software.old.html) but no longer distributed



### [Which kinds of programs are and are not listed](https://evolution.gs.washington.edu/phylip/software.not.html)



## [Other lists of phylogeny software](https://evolution.gs.washington.edu/phylip/software.html#otherlists)



## [New programs waiting to be added](https://evolution.gs.washington.edu/phylip/software.html#new)



-----






|                                            |

| ------------------------------------------ |

| **Table of contents by methods available** |








-----



 **General-purpose

packages**



  - [PHYLIP](https://evolution.gs.washington.edu/phylip/software.pars.html#PHYLIP)

  - [PAUP\*](https://evolution.gs.washington.edu/phylip/software.pars.html#PAUP)

  - [MEGA](https://evolution.gs.washington.edu/phylip/software.pars.html#MEGA)

  - [Phylo\_win](https://evolution.gs.washington.edu/phylip/software.etc1.html#Phylo_win)

  - [ARB](https://evolution.gs.washington.edu/phylip/software.etc2.html#ARB)

  - [DAMBE](https://evolution.gs.washington.edu/phylip/software.pars.html#DAMBE)

  - [PAL](https://evolution.gs.washington.edu/phylip/software.pars.html#PAL)

  - [Bionumerics](https://evolution.gs.washington.edu/phylip/software.pars.html#Bionumerics)

  - [Mesquite](https://evolution.gs.washington.edu/phylip/software.pars.html#mesquite)

  - [PaupUp](https://evolution.gs.washington.edu/phylip/software.pars.html#PaupUp)

  - [BIRCH](https://evolution.gs.washington.edu/phylip/software.etc2.html#BIRCH)

  - [Bosque](https://evolution.gs.washington.edu/phylip/software.etc2.html#Bosque)

  - [EMBOSS](https://evolution.gs.washington.edu/phylip/software.dist.html#EMBOSS)

  - [phangorn](https://evolution.gs.washington.edu/phylip/software.etc2.html#phangorn)

  - [Bio++](https://evolution.gs.washington.edu/phylip/software.pars.html#Bio++)

  - [ETE](https://evolution.gs.washington.edu/phylip/software.pars.html#ETE)

  - [DendroPy](https://evolution.gs.washington.edu/phylip/software.pars.html#DendroPy)

  - [SeaView](https://evolution.gs.washington.edu/phylip/software.etc1.html#SeaView)

  - [Crux](https://evolution.gs.washington.edu/phylip/software.pars.html#Crux)



**Parsimony programs**








**Distance matrix methods**












**Computation of distances**










**Maximum likelihood methods**












**Bayesian inference methods**








**Quartets methods**



  - [TREE-PUZZLE](https://evolution.gs.washington.edu/phylip/software.etc1.html#TREE-PUZZLE)

  - [SplitsTree](https://evolution.gs.washington.edu/phylip/software.etc1.html#SplitsTree)

  - [PHYLTEST](https://evolution.gs.washington.edu/phylip/software.dist.html#PHYLTEST)

  - [GEOMETRY](https://evolution.gs.washington.edu/phylip/software.etc1.html#GEOMETRY)

  - [PICA](https://evolution.gs.washington.edu/phylip/software.etc2.html#PICA)

  - [Darwin](https://evolution.gs.washington.edu/phylip/software.dist.html#Darwin)

  - [PhyloQuart](https://evolution.gs.washington.edu/phylip/software.etc1.html#PhyloQuart)

  - [Willson quartets

    programs](https://evolution.gs.washington.edu/phylip/software.etc1.html#Willson)

  - [Gambit](https://evolution.gs.washington.edu/phylip/software.etc1.html#Gambit)

  - [IQPNNI](https://evolution.gs.washington.edu/phylip/software.etc1.html#IQPNNI)

  - [STC](https://evolution.gs.washington.edu/phylip/software.dist.html#STC)

  - [Quartet

    Suite](https://evolution.gs.washington.edu/phylip/software.etc2.html#Quartet_Suite)

  - [LEVEL2](https://evolution.gs.washington.edu/phylip/software.etc1.html#LEVEL2)

  - [Bosque](https://evolution.gs.washington.edu/phylip/software.etc2.html#Bosque)



**Artificial-intelligence and genetic algorithms

methods**



  - [PTP](https://evolution.gs.washington.edu/phylip/software.etc2.html#PTP)

  - [GAPars](https://evolution.gs.washington.edu/phylip/software.pars.html#GAPars)

  - [MetaPIGA](https://evolution.gs.washington.edu/phylip/software.etc2.html#MetaPIGA)

  - [GARLI](https://evolution.gs.washington.edu/phylip/software.etc2.html#GARLI)



**Invariants (or Evolutionary Parsimony)

methods**



  - [PHYLIP](https://evolution.gs.washington.edu/phylip/software.pars.html#PHYLIP)

  - [PAUP\*](https://evolution.gs.washington.edu/phylip/software.pars.html#PAUP)

  - [PaupUp](https://evolution.gs.washington.edu/phylip/software.pars.html#PaupUp)

  - [BIRCH](https://evolution.gs.washington.edu/phylip/software.etc2.html#BIRCH)

  - [EMBOSS](https://evolution.gs.washington.edu/phylip/software.dist.html#EMBOSS)



**Interactive tree manipulation**








**Looking for hybridization or recombination

events**






**Bootstrapping and other measures of

support** (for Bayesian support methods see the [Bayesian

inference

list](https://evolution.gs.washington.edu/phylip/software.html#Bayesian)

above).










**Compatibility analysis**



  - [COMPROB](https://evolution.gs.washington.edu/phylip/software.etc2.html#COMPROB)

  - [PHYLIP](https://evolution.gs.washington.edu/phylip/software.pars.html#PHYLIP)

  - [PICA](https://evolution.gs.washington.edu/phylip/software.etc2.html#PICA)

  - [partimatrix](https://evolution.gs.washington.edu/phylip/software.etc1.html#partimatrix)

  - [PPH](https://evolution.gs.washington.edu/phylip/software.etc1.html#PPH)

  - [Spectronet](https://evolution.gs.washington.edu/phylip/software.etc1.html#Spectronet)

  - [BIRCH](https://evolution.gs.washington.edu/phylip/software.etc2.html#BIRCH)

  - [EMBOSS](https://evolution.gs.washington.edu/phylip/software.dist.html#EMBOSS)

  - [Murka](https://evolution.gs.washington.edu/phylip/software.pars.html#Murka)

  - [Phybase](https://evolution.gs.washington.edu/phylip/software.etc2.html#Phybase)

  - [TIGER](https://evolution.gs.washington.edu/phylip/software.etc1.html#TIGER)



**Consensus trees, subtrees, supertrees, and

distances between trees**








**Tree-based sequence alignment**



  - [TreeAlign](https://evolution.gs.washington.edu/phylip/software.etc1.html#TreeAlign)

  - [ClustalW](https://evolution.gs.washington.edu/phylip/software.etc1.html#ClustalW)

  - [MALIGN](https://evolution.gs.washington.edu/phylip/software.etc1.html#MALIGN)

  - [GeneDoc](https://evolution.gs.washington.edu/phylip/software.etc1.html#GeneDoc)

  - [DAMBE](https://evolution.gs.washington.edu/phylip/software.pars.html#DAMBE)

  - [POY](https://evolution.gs.washington.edu/phylip/software.etc1.html#POY)

  - [ALIGN](https://evolution.gs.washington.edu/phylip/software.etc1.html#ALIGN)

  - [DNASIS](https://evolution.gs.washington.edu/phylip/software.etc1.html#DNASIS)

  - [FootPrinter](https://evolution.gs.washington.edu/phylip/software.pars.html#FootPrinter)

  - [ALIFRITZ](https://evolution.gs.washington.edu/phylip/software.etc1.html#ALIFRITZ)

  - [T-Coffee](https://evolution.gs.washington.edu/phylip/software.etc1.html#T-Coffee)

  - [ArboDraw](https://evolution.gs.washington.edu/phylip/software.etc2.html#ArboDraw)

  - [BAli-Phy](https://evolution.gs.washington.edu/phylip/software.etc1.html#BAli-Phy)

  - [Geneious](https://evolution.gs.washington.edu/phylip/software.etc2.html#Geneious)

  - [BIRCH](https://evolution.gs.washington.edu/phylip/software.etc2.html#BIRCH)

  - [MAFFT](https://evolution.gs.washington.edu/phylip/software.etc1.html#MAFFT)

  - [LOBSTER](https://evolution.gs.washington.edu/phylip/software%20etc1.html#SATCHMO)

  - [DART](https://evolution.gs.washington.edu/phylip/software.etc2.html#DART)

  - [MUSCLE](https://evolution.gs.washington.edu/phylip/software.etc1.html#MUSCLE)

  - [Bosque](https://evolution.gs.washington.edu/phylip/software.etc2.html#Bosque)

  - [EMBOSS](https://evolution.gs.washington.edu/phylip/software.dist.html#EMBOSS)

  - [SeaView](https://evolution.gs.washington.edu/phylip/software.etc1.html#SeaView)

  - [SuiteMSA](https://evolution.gs.washington.edu/phylip/software.etc2.html#SuiteMSA)



**Gene duplication and genomic analysis**



  - [DERANGE2](https://evolution.gs.washington.edu/phylip/software.dist.html#DERANGE2)

  - [FORESTER](https://evolution.gs.washington.edu/phylip/software.etc2.html#FORESTER)

  - [BPAnalysis](https://evolution.gs.washington.edu/phylip/software.etc1.html#BPAnalysis)

  - [Notung](https://evolution.gs.washington.edu/phylip/software.etc1.html#Notung)

  - [TopD/fMts](https://evolution.gs.washington.edu/phylip/software.etc2.html#TopD/fMts)

  - [DTscore](https://evolution.gs.washington.edu/phylip/software.etc1.html#DTscore)

  - [DART](https://evolution.gs.washington.edu/phylip/software.etc2.html#DART)

  - [gtp](https://evolution.gs.washington.edu/phylip/software.etc1.html#gtp)

  - [EvolSimulator](https://evolution.gs.washington.edu/phylip/software.etc2.html#EvolSimulator)

  - [DTdraw](https://evolution.gs.washington.edu/phylip/software.etc2.html#DTdraw)

  - [Mgenome](https://evolution.gs.washington.edu/phylip/software.etc1.html#Mgenome)

  - [Tree

    Tracker](https://evolution.gs.washington.edu/phylip/software.etc1.html#Tree%20Tracker)

  - [bms\_runner](https://evolution.gs.washington.edu/phylip/software.etc2.html#bms_runner)

  - [MANTiS](https://evolution.gs.washington.edu/phylip/software.etc1.html#MANTiS)

  - [ETE](https://evolution.gs.washington.edu/phylip/software.pars.html#ETE)

  - [MANTiS](https://evolution.gs.washington.edu/phylip/software.etc1.html#MANTiS)

  - [iGTP](https://evolution.gs.washington.edu/phylip/software.etc1.html#iGTP)



**Biogeographic analysis and host-parasite

comparison**



  - [COMPONENT](https://evolution.gs.washington.edu/phylip/software.etc1.html#COMPONENT)

  - [TREEMAP](https://evolution.gs.washington.edu/phylip/software.etc1.html#TREEMAP)

  - [DIVA](https://evolution.gs.washington.edu/phylip/software.etc1.html#DIVA)

  - [TreeFitter](https://evolution.gs.washington.edu/phylip/software.etc1.html#TreeFitter)

  - [GEODIS](https://evolution.gs.washington.edu/phylip/software.pars.html#GEODIS)

  - [Tarzan](https://evolution.gs.washington.edu/phylip/software.etc1.html#Tarzan)

  - [ParaFit](https://evolution.gs.washington.edu/phylip/software.etc1.html#ParaFit)

  - [Phylocom](https://evolution.gs.washington.edu/phylip/software.etc2.html#Phylocom)

  - [AxParafit](https://evolution.gs.washington.edu/phylip/software.etc1.html#AxParafit)

  - [GenGIS](https://evolution.gs.washington.edu/phylip/software.etc2.html#GenGIS)

  - [S-DIVA](https://evolution.gs.washington.edu/phylip/software.etc1.html#S-DIVA)

  - [Lagrange](https://evolution.gs.washington.edu/phylip/software.etc1.html#Lagrange)

  - [CoRe-PA](https://evolution.gs.washington.edu/phylip/software.etc1.html#CoRe-PA)

  - [Jane](https://evolution.gs.washington.edu/phylip/software.etc1.html#Jane)



**Comparative method analysis**








**Simulation of trees or data**








**Examination of shapes of trees**



  - [MacroCAIC](https://evolution.gs.washington.edu/phylip/software.etc2.html#MacroCAIC)

  - [Genie](https://evolution.gs.washington.edu/phylip/software.etc2.html#Genie)

  - [PAL](https://evolution.gs.washington.edu/phylip/software.pars.html#PAL)

  - [Vanilla](https://evolution.gs.washington.edu/phylip/software.pars.html#Vanilla)

  - [RadCon](https://evolution.gs.washington.edu/phylip/software.etc2.html#RadCon)

  - [BRANCHLENGTH](https://evolution.gs.washington.edu/phylip/software.etc2.html#branchlength)

  - [APE](https://evolution.gs.washington.edu/phylip/software.etc2.html#APE)

  - [Tracer](https://evolution.gs.washington.edu/phylip/software.etc1.html#Tracer)

  - [SymmeTREE](https://evolution.gs.washington.edu/phylip/software.dist.html#SymmeTREE)

  - [TreeScan](https://evolution.gs.washington.edu/phylip/software.etc2.html#treescan)

  - [MESA](https://evolution.gs.washington.edu/phylip/software.etc2.html#MESA)

  - [apTreeshape](https://evolution.gs.washington.edu/phylip/software.etc2.html#apTreeshape)

  - [TreeStat](https://evolution.gs.washington.edu/phylip/software.etc2.html#TreeStat)

  - [CTree](https://evolution.gs.washington.edu/phylip/software.dist.html#CTree)

  - [Phyutility](https://evolution.gs.washington.edu/phylip/software.etc2.html#Phyutility)

  - [laser](https://evolution.gs.washington.edu/phylip/software.etc1.html#laser)

  - [PhyRe](https://evolution.gs.washington.edu/phylip/software.etc2.html#PhyRe)

  - [Bio::Phylo](https://evolution.gs.washington.edu/phylip/software.pars.html#Bio::Phylo)



**Clocks, dating and stratigraphy**








**Model Selection**



  - [Modeltest](https://evolution.gs.washington.edu/phylip/software.etc1.html#Modeltest)

  - [MrMTgui](https://evolution.gs.washington.edu/phylip/software.etc1.html#MrMTgui)

  - [MrModeltest](https://evolution.gs.washington.edu/phylip/software.etc1.html#MrModeltest)

  - [Porn\*](https://evolution.gs.washington.edu/phylip/software.etc1.html#Porn*)

  - [ModelGenerator](https://evolution.gs.washington.edu/phylip/software.etc1.html#ModelGenerator)

  - [ProtTest](https://evolution.gs.washington.edu/phylip/software.etc1.html#ProtTest)

  - [MrAIC](https://evolution.gs.washington.edu/phylip/software.etc1.html#MrAIC)

  - [Modelfit](https://evolution.gs.washington.edu/phylip/software.etc1.html#Modelfit)

  - [DT-ModSel](https://evolution.gs.washington.edu/phylip/software.etc1.html#DT-ModSel)

  - [BayesTraits](https://evolution.gs.washington.edu/phylip/software.etc2.html#BayesTraits)

  - [Kakusan4](https://evolution.gs.washington.edu/phylip/software.etc1.html#Kakusan)

  - [MAPPS](https://evolution.gs.washington.edu/phylip/software.etc1.html#MAPPS)

  - [DART](https://evolution.gs.washington.edu/phylip/software.etc2.html#DART)

  - [Concaterpillar](https://evolution.gs.washington.edu/phylip/software.etc1.html#Concaterpillar)

  - [Statio](https://evolution.gs.washington.edu/phylip/software.dist.html#STATIO)

  - [jMODELTEST](https://evolution.gs.washington.edu/phylip/software.etc1.html#jMODELTEST)



**Description or prediction of data from

trees**



  - [CONSERVE](https://evolution.gs.washington.edu/phylip/software.etc2.html#CONSERVE)

  - [TreeDis](https://evolution.gs.washington.edu/phylip/software.etc2.html#TreeDis)

  - [EDIBLE](https://evolution.gs.washington.edu/phylip/software.etc1.html#EDIBLE)

  - [RIND](https://evolution.gs.washington.edu/phylip/software.etc2.html#RIND)

  - [Jevtrace](https://evolution.gs.washington.edu/phylip/software.etc2.html#Jevtrace)

  - [SIMMAP](https://evolution.gs.washington.edu/phylip/software.etc1.html#SIMMAP)

  - [TreeSAAP](https://evolution.gs.washington.edu/phylip/software.etc2.html#TreeSAAP)

  - [DIVERGE](https://evolution.gs.washington.edu/phylip/software.etc2.html#DIVERGE)

  - [MESA](https://evolution.gs.washington.edu/phylip/software.etc2.html#MESA)

  - [FASTML](https://evolution.gs.washington.edu/phylip/software.etc1.html#FASTML)



**Tree plotting/drawing**










**Sequence management/job submission**








**Teaching about phylogenies**



  - [Phylogenetic

    Investigator](https://evolution.gs.washington.edu/phylip/software.etc2.html#Phylogenetic%20Investigator)

  - [Phylap](https://evolution.gs.washington.edu/phylip/software.etc2.html#Phylap)

  - [Dnatree](https://evolution.gs.washington.edu/phylip/software.etc2.html#Dnatree)

  - [SimpleClade](https://evolution.gs.washington.edu/phylip/software.etc2.html#SimpleClade)



-----






Table of contents by computer systems


on which they work



### [Unix (source code in C or executables)](https://evolution.gs.washington.edu/phylip/so