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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: about 6 hours 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/software.html#Unix)



### [Multiplatform interpreters (Java, Perl, Python, R, MATLAB)](https://evolution.gs.washington.edu/phylip/software.html#interpreters)



### 



### [PC's](https://evolution.gs.washington.edu/phylip/software.html#PCs)



### ... [under Windows](https://evolution.gs.washington.edu/phylip/software.html#Windows)



### ... [under DOS or in a Windows Command tool "DOS box"](https://evolution.gs.washington.edu/phylip/software.html#DOS)



### [Macintoshes (under Mac OS X or Mac OS)](https://evolution.gs.washington.edu/phylip/software.html#Macintosh)



### [**e-mail or Web servers** that can analyze data for you](https://evolution.gs.washington.edu/phylip/software.serv.html)



-----



  - **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.

    

    

    

    

    

    

    

    

    

    

    

    


    

    

    

    

    

    

     

    

    

    

    

    

    

    

    

    

    

    

    

    

     

    

    

    

    

    

    

    

    

    

    

    

    

    

    



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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

        

        

        

        

        

        

        

        

        

        

        


        

        

        

        

        

        

         

        

        

        

        

        

        

        

        

        

        

        

        

        

        

      - **under DOS** (MSDOS, PCDOS) or in a

        Command Prompt accessory "DOS box" in Windows

        

        

        

        

        

        

        

        

        

        

        

        

        

        



  - **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.

    

    

    

    

    

    

    

    

    

    

    

    

    


    

    

    

    

    

    

    

     

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    



-----






|                                        |

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

| **Analyzing particular types of data** |



Here you will find lists of programs that analyze types of data other

than molecular sequence data. We will gradually expand this list of data

types.



Microsatellite data    



RAPDs, RFLPs, or AFLPs    



Continuous quantitative    


characters



Gene frequencies


(aside from microsatellite loci)




(under construction: more coming soon)



-----






|                     |

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

| **Recent listings** |



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

the "waiting list" area listing programs that are to be added. You can

use the submission form

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

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).
    • 




-----






|                    |

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

| **Recent changes** |



**Here are the packages whose entries have most recently been changed:**

The date on which each change was entered is shown. Entries are retained

in this list for 6 months. (Note that changes may be as small as updated

version numbers or a modified web address). The most recent changes are

first.



    

  • 

    LVB (19 June 2014)
    • 




-----






|                                       |

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

| **Other lists of phylogeny software** |



  - 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](http://evolution.gs.washington.edu/phylip/software.html)

    instead.

  - Sergios-Orestis Kolokotronis has posted [an extensive

    table](http://research.amnh.org/users/koloko/softlinks/phylogeny.html)

    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](http://en.wikipedia.org/wiki/List_of_sequence_alignment_software)

    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](http://bioinf.man.ac.uk/robertson/recombination/programs.shtml)

    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](http://rintintin.colorado.edu/~robeson/Bioinformatics/OS%20X%20Software%20%26%20Links.html).

  - The Bioinformatics Organization, a nonprofit group in Hudson,

    Massachusetts, has posted the

    [**bioinformatics.org**](http://www.bioinformatics.org/) web pages.

    These offer a free membership and host open source software projects

    in bioinformatics. They also have a [Molecular

    Linux](http://bioinformatics.org/software/mol_linux.php3) 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](http://en.wikipedia.org/wiki/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](http://www.ucmp.berkeley.edu/subway/phylo/phylosoft.html)

    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](http://www.bioinformatik.de/cgi-bin/browse/Catalog/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](http://bioinfo.unice.fr/biodiv/Tree_editors.html) 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](http://www.ib.usp.br/~silvionihei/programas.htm) in

    Portugese. It concentrates on a small number of programs that mostly

    use parsimony methods.



Don Gilbert, of the Department of Biology of the University of Indiana,

has a good web page on [Free Software in Molecular Biology for Macintosh

and MS Windows

computers](http://iubio.bio.indiana.edu/soft/molbio/Listings.html) as of

1998 at `http://iubio.bio.indiana.edu/soft/molbio/Listings.html`. It

lists some popular packages and all packages and programs kept at the

IUBio ftp server at that time (see [our description of that

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

Unfortunately the web links on that page are not active so the addresses

must be copied out and pasted into the URL box of your browser.



Genamics, a company located in Hamilton, New Zealand, maintains the

[SoftwareSeek searchable index of bioinformatics

software](http://genamics.com/software/index.htm) 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](http://evolution.gs.washington.edu/cgi-bin/software-form.pl) 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](http://homes.bio.psu.edu/people/faculty/nei/software.htm),

    intended to estimate positive and negative selection at a single

    amino acid site.



These are not from the Nei site:



  - [PhyRe](http://www.mozoolab.net/index.php/software-download.html)

    infers adequacy of taxon sampling for phylogenetic studies.

  - [phylobase](http://cran.r-project.org/web/packages/phylobase/index.html)

    is an R package that contains a class of functions for comparative

    methods, incorporating one or more trees and trait data.

  - [PhyML-mixtures](http://www.atgc-montpellier.fr/models/index.php?model=mixture),

    a PhyML version for mixture of amino acid models (EX2, EX3, EHO,

    UL2, and UL3).

  - [PhyD\*](http://www.atgc-montpellier.fr/phyd/), Fast NJ-like

    algorithms to deal with incomplete distance matrices.

  - [SDM](http://www.atgc-montpellier.fr/sdm/) a fast distance-based

    approach for tree and supertree building in phylogenomics.

  - [SSIMUL](http://www.atgc-montpellier.fr/ssimul/) does speciation

    signal extraction from multigene families.

  - [Clearcut](http://bioinformatics.hungry.com/clearcut/) carries out

    Relaxed Neighbor Joining (RNJ), a faster NJ-like distance method.

  - [MP-EST](http://code.google.com/p/mp-est/) (also described

    [here](http://cars.desu.edu/faculty/lliu/research/mpest.html)) uses

    trees from different loci to infer a species tree by a

    pseudo-maximum-likelihood method.

  - [TreeRogue](https://stat.ethz.ch/pipermail/r-sig-phylo/2010-October/000816.html),

    an R script for getting trees from published figures of them.

  - [Serial NetEvolve](http://biorg.cis.fiu.edu/SNE/) simulation program

    evolves serially-sampled sequences with or without recombination.

  - [Rococo](http://bibiserv.techfak.uni-bielefeld.de/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](http://evolution.gs.washington.edu/cgi-bin/software-form-new1.pl)

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](http://groups.yahoo.com/group/SB1981/files/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](http://www.uhnresearch.ca/labs/tillier/software.htm) uses

    Multiple Interdependency to detect functional interactions between

    amino acids in proteins. Does not seem to actually use a phylogeny.

  - [Codep](http://www.uhnresearch.ca/labs/tillier/software.htm)

    Maximizes co-evolutionary interdependencies to discover interacting

    proteins. Also does not seem to actually use a phylogeny.

  - [PhyloGrapher](http://www.atgc.org/PhyloGrapher/Graph_Ath_NBS.html)

    shows clustering relationships between genes in a genome based on a

    distance matrix. But is it a phylogeny program?

  - [Phylosopher](http://www.genedata.com/products/phylosopher/index_eng.html)

    commercial package for functional genomics said to include some

    phylogeny functions. Does it?

  - [Phylogenator](http://www.multimedialibrary.com/Articles/Jack/Phylogenator.asp)

    server displaying aligned sequences -- does it actually use or

    construct phylogenies?

  - [MultiLocus](http://www.agapow.net/software/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](http://www.phylo.org/sub_sections/software/)

    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.



-----



[To first page of main software

listing](https://evolution.gs.washington.edu/phylip/software.pars.html)



-----



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the PHYLIP home page](https://evolution.gs.washington.edu/phylip.html)

  







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