- Phylip software, free download Winzip
- Phylip software, free download Windows 10
- Phylip software, free download Windows 8
- Phylip software, free download Camtasia
- Phylip software, free download Version
- Phylip software, free download Mac
- PHYLogeny Inference Package (PHYLIP) is a free computational phylogenetics package of programs for inferring evolutionary trees (phylogenies). It consists of 35 portable programs, i.e., the source code is written in the programming language C.As of version 3.696, it is licensed as open-source software; versions 3.695 and older were proprietary software freeware.
- Kevin Nixon has withdrawn ClaDOS: it is replaced by his more recent program WINCLADA which incorporates the features of ClaDOS and of another program, DADA. ClaDOS, an interactive program which allow s rearrangement of trees and their evaluation, mapping of characters into them, and more, is available for DOS systems from Kevin Nixon, L. Bailey Hortorium, Cornell University, 467 Mann.
Get me PHYLIP now |
Note -- you probably need the full PHYLIP package, includingthe source code and documents in some form, simply in orderto make sure that you have the documentation, even if you do not intend to ever recompile the sourcecode. Most Windows and MacOS users will want to use theexecutables for theirmachines and will not need to recompile the source code,but everyone will need the documentation as well. Whenever PHYLIPis packaged as a single archive, it does include the all of thesource code and documentation.
TreeView is a free phylogenetic tree viewer software for Windows. In this software, you can open and edit the evolutionary trees of different species. Hence, by analyzing the evolutionary trees, you can study how the process of evolution has taken place in different species. Alternatively, the Windows version of MEGA7 (and earlier) can be ran on macOS by using virtualization software such as VMWareFusion. Disclaimer Although utmost care has been taken to ensure the correctness of the software, the software is provided 'as is' without any warranty of any kind.
The Windows executables, documents, and sourcesare in the form of a Zip archive. To extract it,put it in a directory by itself and right-click on theicon of the archive. You will then be given the option to unpack the archiveinto the many files of the package.
The Mac OS X package is distributed as a .dmg Disk Image whichcan be unpacked using the instructions on our installation web page.The Linux executables can easily be compiledafter downloading the source code -- see the installation page here.
What to do |
First note that at the bottom of this page is a link to registeryour copy of PHYLIP, and also a link to installation instructions.To transfer the files,click on the appropriate links below. Then register, and read theinstallation instructions and follow them.
1. Fetch the following: |
PHYLIP's license is changing to an open-source license. Itnow uses a license that allows re-use in other software packages withoutdemanding a royalty. (It does not demand that all other software in thatdistribution be open-source). The source code tar archive below has the newlicense. I have designated it as a new version, 3.698. |
Linux or Unix
For Linux or Unix (or other systems that need to compile from source code):
(see below for information on how to compile these, and forinformation on precompiled Linux and Unix executables).Windows
We have here the PHYLIP package for Windows, which works onall versions of Windows from Windows 3.1 to Windows 10.Executables, documentation files, andsource code is included in this distribution.
PHYLIP for Windows is available here in two forms. You willneed only one of these, so read carefully before downloading. If youclick on one of these selections to download it, make sure your browsersaves it to disk. Afterdownloading, but before you do anythingelse, you should readour installation instructions.If you have a recent Windows system that is able to extract a ZIPthat file, and if you can transfer a file that is about 12 megabytes in size, you will want to download thiszip archive, and then right-click on it to see an option to unzip thearchive.
- If you have (as most people do) a 64-bit Windows system, use this Zip archive: Zip archive of PHYLIP 3.698 for Windows.
- If you have an older Windows system that is a 32-bit system,
thenyou will need to use this older version that was compiled for 32-bit systems: Zip archive of PHYLIP 3.695 for Windows.
Phylip software, free download Winzip
Mac OS
For Macintosh Mac OS (either Intel iMac or PowerMac) the package is distributed as a single compresseddisk image (.DMG) file of 12 Megabytes. Click on this link to download it:
After PHYLIP is installed, the most recent Mac OS X operating system versions,from Mountain Lion on, may refuse to run its executables when you click on the programicon. There is a good workaround for this -- see the discussion atourinstallation web page.
2. Register your copy |
(It is not necessary to register separately for each file transferred -- youcan register once after downloading several files).
3. Install PHYLIP |
Precompiled executables available elsewhere |
Debian linux executables
Andreas Tille and Manuel Prinz have compiled and made available a set of PHYLIP3.695 executables for Debian Linux.These are in the 'unstable' section of Debian packagesand may be downloaded for free ('free in the sense of free beer') fromits page on the Debian web site at
http://packages.debian.org/unstable/science/phylip
.or from various Debian mirror sites. Of course, one can also installthe source code (see under Unix above) and compile it yourself.Executables for FreeBSD
A PHYLIP 3.695 package for FreeBSD Unix is available, thanks to David Baderand others. It is located atthe BSD PHYLIP package web page at
http://www.freebsd.org/cgi/cvsweb.cgi/ports/biology/phylip/
.Specialized source code versions available elsewhere |
Source distribution for NetBSD
A set of sources and executables for PHYLIP 3.69 forthe NetBSD operating system has been produced (originally by Marc Baudoin). They are available fromThe NetBSD Packages Collection PHYLIP page at
This is access number of the pages for fetching copies of PHYLIPsince 1 January 2020. In 1996 there were 7,905 accesses. (In 1997-1999no count was made). In 2000 there were 21,414 accesses, in 2001there were 27,781, in 2002, 33,652, in 2003, 38,543, in 2004, 44,004,in 2005, 43,033, in 2006, 42,421, in 2007 39,926, in 2008, 38,855, in2009, 35,412, in 2010, 32,560, in 2011, 28,354, in 2012, 26,737,in 2013, 28,671, in 014, 26,933, in 2015, 23,062, and in 2016, 21,681. In2017 no number was collected owing to malfunction of the counting codeduring part of the year. In 2018, there were 16,163 accesses, and in 2019,15,267 accesses.To go to top of the Software pageshttp://ftp.netbsd.org/pub/pkgsrc/current/pkgsrc/biology/phylip/README.html
Tatsuya Ota, most recently at the HayamaInformation Network Center at theGraduate University of Advanced Studies, Hayama, Japan(
ota(at) soken.ac.jp
)written a package,DISPAN, (Genetic Distance and Phylogenetic Analysis),which computes for gene frequency data the heterozygosity, gene diversity, Nei's standard geneticdistance or the DA distance, and their standard error.It also constructs phylogenies using the neighbor-joining (NJ) method or the UPGMA method. These trees can also bebootstrapped. A tree editor allows the user to rearrange the tree and print it out.The package consists of two programs, GNKDST and TREEVIEW. The first is arewrite of a program by A. K. Roychoudhury, Y. Tateno, D. Graur, N. Saitou,and R. Schwartz, the second was written by Koichiro Tamura. DISPANis distributed as DOS executables (which can run under Windows in a Commandtool window. The package and its Readme file are availableat the IUBIO softwareserverat http://iubio.bio.indiana.edu/soft/molbio/ibmpc/
and at aweb page describing it athttp://www.bio.psu.edu/People/Faculty/Nei/Lab/dispan2.htm
at the software pages ofMasatoshi Nei's laboratory at Molecular Evolution and Phylogeneticsat Pennsylvania State University.Kevin Howe, Alex Bateman, and Richard Durbin of the Wellcome Trust SangerInstitute in Hinxton, U.K. (klh(at) sanger.ac.uk, agb (at) sanger.ac.uk,and rd(at) sanger.ac.uk) have released QuickTree,a program for rapid calculation of Neighbor-Joining trees. The algorithmsused are O(n3) like most other implementations of thatmethod, but have been optimized for speed. The program isdescribed in the paper: Howe, K., A. Bateman, and R. Durbin. 2002.QuickTree: building huge Neighbour-Joining trees of protein sequences.Bioinformatics18: 1546-1547. QuickTree is distributed asC source code fromits web site at
http://www.sanger.ac.uk/resources/software/quicktree/
Travis Wheelerof the Janelia Farm Research Campus of the Howard Hughes Medical Institute(travis (at) nimbletwist.com)has released NINJAversion 1.0.4, software for inferring large-scale neighbor-joining phylogenies from distance matrices. NINJA is argued by Wheeler to be the fastest available tool for computing correct neighbor-joining phylogenies for inputs of more than 10,000 sequences, and to be more than 10x faster than the fastest implementation of the canonical neighbor-joining algorithm (QuickTree). It is described in the paper:Wheeler, T. J. 2009. Large-scale neighbor-joining with NINJA. pp. 375-389 inSalzberg , S. L. and T. Warnow (eds.), Proceedings of the 9th Workshop onAlgorithms in Bioinformatics. WABI 2009 Springer, Berlin.It is available as Java source code and Java executables. It can be downloaded fromits web siteat
http://nimbletwist.com/software/ninja/
It isalso available as part of the Mesquite package of Java programs.Sudhir Kumar, (
S.Kumar(at) asu.edu
),of the Center for Evolutionary Functional Genomics at Arizona StateUniversity, Tempe, Arizonahas written PHYLTEST, version 2.0. It is a DOSexecutable program for testing phylogenetic hypotheses about fourclusters of DNA sequences. It implements comparison of three alternativephylogenetic trees for four monophyletic clusters of sequences, thefour-cluster analysis: Rzhetsky, A, S. Kumar, and M. Nei. 1995.Four-cluster analysis: a simple method to test phylogenetic hypotheses.Molecular Biology and Evolution12: 163-167.It can also carry out the interior branch test of the null hypothesis that an interiorbranch length is significantly longer than zero (Rzhetsky, A. and M. Nei. 1992.A simple method for estimating and testing minimum-evolution trees.Molecular Biology and Evolution9: 945-967), aswell as the estimation of average pairwise distances (and standard errors)within and between clusters of sequences andrelative rate tests and the computation of the time of divergence.PHYLTEST is distributed fromthe IUBIO softwareserver at http://iubio.bio.indiana.edu/soft/molbio/ibmpc/
molbio/ibmpc
. The 'readme' file for it is distributed thereand is also available atMasatoshi Nei's lab software pageweb pageat Pennsylvania State University athttp://www.bio.psu.edu/People/Faculty/Nei/Lab/phyltest2.htm
.It is distributed as a self-extracting archive, containing the executables andexamples, with a Readme file. Theprogram can be run under DOS or in the Command tool of Window.TREECON version 1.3b is a software package developed byYves Van de Peer of the Bioinformatics and Evolutionary Genomics group at theDepartment of Plant Systems Biology, University of Ghent, Belgium(
yves.vandepeer(at) @psb.ugent.be
) for theconstruction and drawing of phylogenetic trees based on distance data.Several equations are included to convert dissimilarity into evolutionarydistance and several methods (such as neighbor-joining) are included forinferring the tree topology. It also includes bootstrap analysis. It alsohas good facilities for rerooting and drawing trees. Theprogram is available for free for academic use, for other use youare asked to contact its author. It on PCs under Windows.It is described in several papers:- Van de Peer, Y. and R. De Wachter. 1993. TREECON: a software package forthe construction and drawing of evolutionary trees. Computer Applicationsin the Biosciences (CABIOS)9: 177-182.
- Van de Peer, Y. and R. De Wachter. 1994. TREECON forWindows: a software package for the construction and drawing ofevolutionary trees for the Microsoft Windows environment.Computer Applications in the Biosciences (CABIOS)10: 569-570.
- Van de Peer, Y. and R. De Wachter. 1997. Construction of evolutionarydistance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. Computer Applications in the Biosciences (CABIOS)13: 227-230.
- Van de Peer, Y. 2003. Analysis of nucleotide sequences using TREECON.pp. 236-255 in The Phylogenetic Handbook, edited by M. Salemi and A.-M.Vandamme. Cambridge University Press, Cambridge, U.K.
http://bioinformatics.psb.ugent.be/software_details.php?id=3
, and it can bedownloaded from there, and an online manual is also viewable there.Andrey Rzhetsky (
andrey.rzhetsky(at) dbmi.columbia.edu
) of the Departmentof Biomedical Informatics at Columbia University, New Yorkand Masatoshi Nei of the Institute of Molecular and Evolutionary Genetics at Pennsylvania StateUniversity have producedMETREE version 1.2, a program for carrying out the minimum-evolutiondistance matrix method. METREE runs onDOS systems and on Windows (under a Command Tool window). It computesminimum evolution distance matrix trees from DNA and amino acid sequence dataand tests the statistical significance oftopological differences and of the branch lengths. Different distancematrix measures may be used. The package is menu driven and the TREEVIEWprogram written by Koichiro Tamura forvisualizing and printing out the final tree is also included. The method isdescribed in the paper by A. Rzhetsky and M. Nei. 1992. A simple method forestimating and testing minimum-evolution trees. Molecular Biology andEvolution9: 945-967, and the program is described ina paper by A. Rzhetsky and M. Nei. 1994. METREE: a program package forinferring and testing minimum-evolution trees. Computer Applications inthe Biological Sciences (CABIOS)10: 409-12.METREE is distributed fromthe IUBIOserver from http://iubio.bio.indiana.edu/soft/molbio/ibmpc/
.A Readme file is also available at its listing in its listing atthesoftware page of Masatoshi Nei's laboratory athttp://www.bio.psu.edu/People/Faculty/Nei/Lab/software.htm
Richard Desper, most recently of Ziheng Yang's lab at theDepartment of Biology, University College, London, U.K.,and Olivier Gascuel of the LIRMM (Laboratoire d'Informatique de Robotique et deMicroélectronique de Montpellier), Montpellier, France (gascuel (at)lirmm.fr) have written FastME, a fast program for theminimum evolution distance matrix method. It is described as faster thanneighbor-joining methods, more accurate than them, and as accurate asleast squares methods. It can analyze multiple data sets as part ofbootstrapping analyses. Its methods are described in two papers:
- Desper, R., and O. Gascuel. 2002. Fast and accurate phylogenyreconstruction algorithms based on the minimum-evolution principle.pp. 357-374 in Proceedings of the Second International Workshopon Algorithms in Bioinformatics, WABI 2002, Rome, Italy, September 17-21,2002. ed. R. Guigó and D. Gusfield. LectureNotes in Computer Science, no. 2452. Springer-Verlag, Berlin.
- Desper, R. and O. Gascuel. 2002. Fast and accurate phylogenyreconstruction algorithms based on the minimum-evolution principle.Journal of Computational Biology19: 687-705.
http://www.atgc-montpellier.fr/fastme/binaries.php
.Olivier Gascuel (
gascuel(at) lirmm.fr
) ofthe Laboratoire d'Informatique, de Robotique et de Micro-Electronique deMontpellier (LIRMM) of the Universite de Montpellier II, France has writtenBIONJ, an improved version of Neighbor-Joiningbased on a simple model of sequence data. It follows the same agglomerative scheme as NJ but uses a simple, first-order model of the variances and covariances of evolutionary distance estimates. This model is appropriate when these estimates are obtained from aligned sequences. It retains the speed advantages ofNeighbor-Joining while using a slightly different criterion to selectpairs of taxa to join, one which will perform better when distancesbetween taxa are large. It is described in the paper: Gascuel, O. 1997.BIONJ: An improved version of the NJ algorithm based on a simple modelof sequence data. Molecular Biology and Evolution14: 685-695.C source code and Windows, Linux, and Mac OS X executables of BIONJ areavailable at its web page athttp://www.atgc-montpellier.fr/bionj/binaries.php
.It is also available as a web server here.William J. Bruno of the Los Alamos NationalLaboratory (
billb(at) lanl.gov
) has releasednneighbor, a modification of thePHYLIP Neighbor-Joining distancematrix program that avoids negative branch lengths (its name meansNon-Negative Neighbor). The program is available as generic C code.It is available atone of Bruno'sweb pages athttp://www.t10.lanl.gov/billb/related_links.html
.William J. Bruno, Nicholas D. Socci, and Aaron L. Halpernof the Los Alamos National Laboratory (
billb(at) lanl.gov
) haveproduced weighbor (Weighted nEIGHBOR-joining or perhapsWEIGHted neighBOR-joining), version 1.2.1,a distance matrix program forperforming a weighted version of the Neighbor-Joining method. Theweighting used is for nucleotide sequences and more correctly reflects theuncertainty of the longer distances in the tree than does ordinaryNeighbor-Joining. It is thus closer to approximating maximum likelihoodand will be more accurate than Neighbor-Joining on large trees.It is described in a paper:Bruno, W. J., N. D. Socci, and A. L. Halpern 2000. Weightedneighbor joining: a likelihood-based approach to distance-basedphylogeny reconstruction. Molecular Biology and Evolution17:189-197. Weighboris available as C source code and as Windows, IRIX, Solaris, and Linuxexecutables (plus some older executables for DOS and Mac OS) fromits web siteat http://www.t10.lanl.gov/billb/weighbor/index.html
.It is also available as a web server at the Institut Pasteurin Paris.Paul Lewis, (
plewis(at) uconnvm.uconn.edu
),of the Department of Ecology and EvolutionaryBiology, University of Connecticut, and Dmitri Zaykin, then of North CarolinaState University.have written GDA version 1.1,a set of programs to carry out many of the statistical methods foranalyzing gene frequencies and sequence data that are described inBruce Weir's book Genetic Data Analysis II(Sinauer Associates, Sunderland, Massachusetts, 1996). The programs run underWindows and include the calculation of UPGMA and Neighbor-Joining phylogenies.The program is described in a Web sitemaintained by Paul Lewis athttp://hydrodictyon.eeb.uconn.edu/people/plewis/software.php
There is also a link there to a command-line-only version of GDA byChris Basten that runs under Mac OS X.The relevant feature for the purposes of this listing is the ability ofthe programs to compute a number of distances.Mark Miller (
MarkPerryMiller(at) gmail.com
) of theForest and Rangeland Ecosystem Science Center of the U.S. Geological Surveyhas written TFPGA (Tools For Population GeneticsAnalyses), a Windows program for the analysis of allozyme andmolecular population genetic data. It can calculate genetic distances.In addition, this program calculates descriptive statistics,and F-statistics, and performs tests for Hardy-Weinberg equilibrium, exact tests for geneticdifferentiation, Mantel tests, and UPGMA cluster analyses. Additional features include the abilityto analyze hierarchical data sets as well as data from either codominant markers such as allozymesor dominant markers such as AFLPs or RAPDs. It is available fromhis software web page athttp://www.marksgeneticsoftware.net/
as a Windows executable.François Bonhommeof the Institut des Sciences de l'Evolution of theUniversité de Montpellier, France,along with K. Belkhir, P. Borsa, N. Raufaste and L. Chikhi(the program support email address is
genetix(at) univ-montp2.fr
)has released Genetix version 4.05. This is a Windowsexecutable program that does a wide variety of population geneticprocedures. The part relevant to the present list is that itcomputes the Nei and the Cavalli-Sforza genetic distances, both with andwithout bias correction. It also calculates F statistics and linkagedisequilibrium, and performs permutation tests on the results.One advantage (or limitation, depending on your perspective) is thatthe interface is in French.Genetix is available fromits web site(in French) at http://www.univ-montp2.fr/~genetix/genetix/genetix.htm
.Steven Kalinowski of the Department of Ecologyof Montana State University, Bozeman, Montana(skalinowski (at) montana.edu)has written TreeFitversion of 17 Dec 2007, a program to compare the fit of UPGMA and Neighbor-Joining trees to the same data. TreeFit creates neighbor-joining and UPGMA trees from a genetic distance matrix, and then compares the observed genetic distance between populations with the genetic distance in the tree. The similarity between these distances is express as R-squared, the correlation measure used in regression analyses. TreeFit can take as input either a distance matrix or genotypes in GenePop format. In that case it computes Fst genetic distances itself.It is available as Windows executables.It requires some pieces of the Microsoft .NET framework to run.It can be downloaded fromits web siteat
http://www.montana.edu/kalinowski/Software/TreeFit.htm
Immanuel Yap, now of the Department ofPlant Breeding and Genetics at Cornell University, Ithaca, New York(noelyap(at) ascus.plbr.cornell.edu)and Rebecca Nelson, now of the Department of Plant Breeding and Geneticsand the Department of Plant Pathology and Plant-Microbe Biology, CornellUniversity rjn7 (at) cornell.edu)when they were at theInternational Rice Research Institute in Manila, Philippinesreleased Winboot, a package of two programs for calculatingUPGMA trees forbinary (0/1) data and computing bootstrap support for groups on those trees.The programs can read 0/1 data in either PHYLIP format or a tabbed Excel-likeformat. They can compute a large variety of simple similarity coefficientsand carry out bootstrapping on the input file before doing so. The Winbootprogram uses this to computea bootstrap consensus tree. The Windist program is similar, but instead writesout the bootstrap sampled distance matrices to an output file in PHYLIP orNTSYS format. The package contains somecode from PHYLIP, by agreement.Winboot is available as Windows executables fromits web siteat
http://archive.irri.org/science/software/winboot.asp
.María Jesús Martín and Joaquín Dopazo, then ofthe R&D Department of TDI (TDI-EMBNet), Spain, (Dopazo is now at theBioinformatics Department at the Centro de Investigación Príncipe Felipe(CIPF), Valencia, Spain:jdopazo (at) cipf.es )>tdi.es or
dopazo (at) tdi.es
) have developed OSA (Optimal SequenceAnalysis), version 2.0. It finds, whithin large sequences, those regions with an informationcontent similar to that of the whole sequence and it selects, amongthem, the shortest ones. This program was formerly called ORF.The algorithm used is based on comparing pairwise genetic distances, calculatedfor windows of variable size and position, to thedistance matrix obtained for the whole sequence. Either uncorrectedgenetic distances or Jukes-Cantor distances can be used.Two methods are used to set cutoff levels: simulation-based significancevalues or bootstrapping. A variety of options for search among possiblewindows are available. The method has been described in a paper:M. J. Martín, F. Gonzalez-Candelas, F. Sobrino and J. Dopazo. 1995.A method for determining the position and size of optimal sequence regions forphylogenetic analysis. Journal of Molecular Evolution41: 1128-1138.OSA uses aligned sequences in a number of common formats as input.It runs on UNIX-based machines. It is available in Gnu Pascal source codeand also executable versionsfor Solaris and IRIX operating systems are available.The program can analyze up to 50 sequences of a maximum length of 10,000 bp.It can be obtained by ftpfrom ftp.ebi.ac.uk
in directory pub/software/unix/osa
,where the source code, a documentation file,and the Solaris and Irix executables are available.Johannes Schaefer and Michael Schoeniger, then of theLehrstuhl für Theoretische Chemie of theTechnische Universität Münchenhave written DISTREE. Itcomputes pairwise distances ofaligned nucleotide sequences utilizing various models of basesubstitution. Moreover it provides the user with informationon the goodness of fit of the models to the given set ofsequence data. Each of the models is implemented in twovariants, assuming identical and gamma distributedsubstitution rates across sequence sites.It is available as a DOS executable with C source code, or as source code for Unixsystems.DISTREE is distributed throughthe EBI software site archiveat
http://mirror.pscigrid.gov.ph/ebi-software/software/dos/distree/
,Mikael Thollesson (lddist(at) artedi.ebc.uu.se), of theDepartment of Molecular Evolution, Evolutionary Biology Centre, UppsalaUniversity, Sweden has written LDDist version 1.3.2,which calculates LogDet distances from DNA and protein sequences. Itaccomodates rate variation from site to site as well, by excluding invariantsites or by allowing different rates for different sites to be preassigned.LDDist is described in a paper: Thollesson, M. Mago de oz flac. 2004. LDDist: a Perl module forcalculating LogDet pair-wise distances for protein and nucleotide sequences.Bioinformatics20: 416-418. LDDist is, as this says, writtenin Perl and C++. With it is distributed PLD.pl Vicente amigo morente tabor. , a companion scriptthat serves as a front-end and example of how to use LDDist. They aredistributed in source code fromits web siteat
http://artedi.ebc.uu.se/molev/software/LDDist.html
William J. Bruno and Lars Arvestad(
billb(at) t10.lanl.gov
) of the Theoretical Biology andBiophysics Group at Los Alamos National Laboratory,have released DISTANCE, version 1.0.It estimates the most general reversible substitution matrixcorresponding to a given collection of aligned DNA sequences.This matrix can then be used to calculate evolutionary distances between pairsof sequences. The method is described in a paper:Arvestad, L. and W. J. Bruno. 1997. Estimation of reversible substitutionmatrices from multiple pairs of sequences. Journal of Molecular Evolution45: 696-703. The program is written in C, and distributed fromits web site athttp://www.t10.lanl.gov/evolution/
, along with Sun SPARCbinaries.Joyce Miller Hersh (
msmead(at) doctorbeer.com
),formerly of the Whitehead Institute at MIT (and more recently a high-techpatent attorney) wrote RESTSITE, version 1.2,a package of DOS programs for computing distances between species based onrestriction sites or restriction fragments. The programs also includeNJTREE and UPGMA which can infer phylogenies by the Neighbor-Joining andUPGMA distance matrix methods. The programs are written in Microsoft C:source code is available too. The programs, documentation, and source code are distributed byits Web site, http://www-genome.wi.mit.edu/~jmiller/restsite.htm
.The programs and their methods were described in two papers:- Miller, J. C. 1991. RESTSITE: A phylogenetic program that sortsraw restriction data. Journal of Heredity82: 262-263.
- Nei, M., and J. C. Miller. 1990. A simple method for estimating averagenumber of nucleotide substitutions within and between populations fromrestriction data. Genetics125: 873-879.
Doug McElroy (
Doug.McElroy(at) wku.edu
) of Western Kentucky University distributes REAP, theRestriction Enzyme Analysis Package, written by him, Paul Moran, EldredgeBermingham, and Irv Kornfeld. REAP can calculate distances from restriction sites,restriction fragments data, and from nucleotide sequences (the Kimura2-parameter distance). REAP is a package of DOS executables availablefrom McElroy's web site.at http://bioweb.wku.edu/faculty/mcelroy/
.It is described in the paper:McElroy, D., P. Moran, E. Bermingham, and I. Kornfield. 1992. REAP: An integrated environmentfor the manipulation and phylogenetic analysis of restriction data.Journal of Heredity83: 157-158.![Software Software](https://www.researchgate.net/profile/Priscila_Chaverri/publication/338446053/figure/download/fig5/AS:882853051129857@1587499978583/Example-for-Phylip-file-structure.png)
Peter Rice, Alan Bleasby, and Jon Isonof the European Bioinformatics Institutein Hinxton, England(emboss (at) emboss.open-bio.org)have produced EMBOSS(European Molecular Biology Open Software Suite),version 6.0.1, a package of programs for general sequence analysis with phylogeny and alignment programs. EMBOSS, developed by many developers, is a general suite of programs for sequence analysis. It is a full-featured sequence analysis program developed intended to provide the samefunctionality as GCG. In additionto its own programs, it also has a suite of other programs, EMBASSY, thatare configured to work with EMBOSS. These includeClustalW and most PHYLIP programs. EMBOSS and EMBASSY are a properly constructed toolkit for creating robust bioinformatics applications or workflows, with a comprehensive set of sequence analysis programs. All sequence and many alignment and structural formats are handled.There is an extensive programming library for common sequence analysis tasks. Several different GUI interfaces for it are available.It is described in the paper:Rice, P., I. Longden, and A. Bleasby. 2000. EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics16 (6): 276-277.It is available as C++ source code and C source code. It can be compiled onall known Unix and Linux systems. It can be downloaded from its web siteat
http://emboss.sourceforge.net/what/
MacVector, Inc., PMB 150, PO Box 582, 1939 High HouseRd., Cary, NC 27519 and PO Box 582, Cambridge, U.K. CB1 0FH(info (at) macvector.com)sells MacVector version 10.0.2, asequence analysis program for Mac OS and Mac OS X systems. The features thatare relevant for this listing are its ability to doalignment and produce a guide treeusing ClustalW, andeither UPGMA or Neighbor-Joining distance matrix methods. It has many otherfeatures including sequence search, gene finding, motif searching,protein secondary structureand hydrophobicity prediction, and prediction of restriction digests andprimer sites. Version 7.2 onwards can run natively on Mac OS X systems.It can be ordered throughits web pageat
http://www.macvector.com
. Itsprice for academic use was formerly $2,500, and for commercial use $5,000.Currently they do not give prices on their web page, but they have said tome that the above is slightly more expensive than what they charge now.Soll Technologies, Inc., (sales(at) solltechnologies.com)321 Lexington Ave., Iowa City, Iowa 52246,USA distributes DENDRON, acomputer-assisted system for Windows for analyzing DNA fingerprinting gels. Itreads and compares gel images. One feature is an average-linkage clustering algorithm that can produce trees from the gel images. For information and pricing, contact Soll Technologies. The DENDRONweb page isat
http://www.solltechnologies.com/products.html
.Philipp Schlüterof the Institut für Systematische Botanikof the University of Zürich, Switzerland(philipp.schlueter (at) systbot.uzh.ch)distributes FAMD (Fingerprint Analysis with Missing Data),version 1.108, a program for the analysis of dominant fingerprint data (AFLP, RAPD, etc.). It has a graphical user interface and functions for calculating distances among individuals (Jaccard, Dice, SMC, Nei and Li, Euclidean) or populations (CSE chord distance, pairwise PhiST), as well as tree building (UPGMA, NJ), consensus tree, and principal coordinate analysis routines including a flexible 3D viewer. FAMD handles missing data and allows the user to investigate the impact of missing data on the analyses. It contains routines for data matrix management (e.g. data filtering, easy management of groups/populations) and export filters to other programs' file formats (e.g., Nexus, Arlequin, Hindex, Hickory,GenePop/BAPS,NTSYSpc, Structure, Dfdist). It can calculate Shannon's index, estimate its variance by bootstrapping, perform AMOVA and Bayesian estimation of null allele frequencies.The methods are described in the paper:Schlüter, P. M. and S. A. Harris. 2006. Analysis of multilocus fingerprinting data setscontaining missing data. Molecular Ecology Notes6: 569-572.It is available as Windows executables. It can be downloaded fromits web siteat
http://www.famd.me.uk/famd.html
James McInerney of the Department of Biology of theNational University of Ireland, Maynooth, County Kildare, Ireland(james.o.mcinerney(at) may.ie)has written GCUA(General Codon Usage Analysis). It does codon usage and amino acid usagestatistics, and also performs correspondence analysis/principle componentsanalysis on both codon usage and amino acid usage statistics. Itsrelevance to the present list is that it also produces a distance matrix,based on Relative Synonymous Codon Usage (RSCU) statistics, whose format isPHYLIP/PAUP*4.0 -compatible. Although McInerney cautions that this matrixshould not be used for phylogenetic inference, I wonder whether thisdistance does not have some phylogenetic information.The program is described in the paper: McInerney, J. O. 1998. GCUA (GeneralCodon Usage Analysis). Bioinformatics14 (4): 372-373.It is available as Mac OS X, Mac OS, Windows, IBM AIX, Digital Unix, andLinux binaries.The code isn't available, he says 'because it is so embarassingly poor'.It is available at his softwaredownloads site at
http://bioinf.nuim.ie/downloads.html
.Earlier binaries, version 1.1 for Digital Unix, SunOS, Mac OS and Irixand version 1.2 for Linux, Digital Unix, Mac OS and SunOScan be retrieved via anonymous ftpfrom ftp.nhm.ac.uk
in directory pub/gcua
David T. Pride (dpride (at) partners.org),formerly of Vanderbilt University (currently an internal medicine specialistin Berkeley, California), has written Swaap version1.02. Swaap performs sliding window analyses on nucleotide sequences, computinga large variety of statistics on the sequences. The relevant feature forthis listing is the ability to compute four different distance measuresbetween sequences, either on full sequences or on sliding windows.Swaap is distributed as a Windows executable fromthe Swaapand Swaap PH web siteat
http://www.bacteriamuseum.org/SWAAP/SwaapPage.htm#Swaap
David T. Pride (dpride (at) partners.org),formerly of Vanderbilt University (currently an internal medicine specialistin Berkeley, California), has written Swaap PH version1.02. Swaap PH computes many different kinds of statistics on nucleotidefrequencies and oligonucleotide frequencies in sliding windows alongnucleotide sequences. It can compute distances based on these frequencies.Swaap PH is a a Windows executable available fromthe Swaap and Swaap PH web siteat
http://www.bacteriamuseum.org/SWAAP/SwaapPage.htm#Swaap
Mathieu Blanchette of the McGill University Centre forBioinformatics (
blanchem(at) mcb.mcgill.ca
) and David Sankoffof the Department of Mathematics and Statistics of the University ofOttawa, Canadahave produced DERANGE2, a program to reconstruct thehistory of two gene maps using weighted inversions, transpositionsand inverted transpositions. It can thus construct a set of distancesbased on the gene orders (not the sequences of the genes themselves).It is available as a standard C source code and can readily be compiled on Unix systems. It is availableby anonymous ftpfrom ftp.ebi.ac.uk
in directory pub/software/unix
.Laurent Excoffier of theComputational and Population Genetics Lab of the Institute of Zoology,University of Bern, Switzerland(laurent.excoffier(at) zoo.unibe.ch)has producedMINSPNET, a program that produces a minimum spanning treeand network from a distance matrix. It is available as a Windowsexecutable. It can be obtained froma web page which lists software from that lab at http://cmpg.unibe.ch/software.htm.
Francis Yeh (
francis.yeh(at) ualberta.ca
) of theDepartment of Renewable Resources at the University of Alberta, Canada, hasreleased POPGENE version 1.32, a free program for the analysis of geneticvariation among and within populations using co-dominant and dominant markers.The feature that is relevant to the present list is that it can computea number of genetic distances for gene frequencies.It is distributed as a Windows executable fromits home page athttp://www.ualberta.ca/~fyeh/index.htm
. F. James Rohlf has written NTSYSpc(Numerical Taxonomy System, Version 2.2), a clustering program thatincludes calculation of various kinds of distance measures, as well asHierarchical clustering methods such as UPGMA as well as Neighbor-Joiningand consensus trees. It can also do a variety of other things includingordination, scatter diagrams, and elliptic Fourier transforms (for shapeanalysis). NTSYSpc 2.1 is a Windows95 executable which will also run onWindows NT. It is available for $350 ($250 for educational and governmentinstitutions). 10-user site licensese are also available. It isdistrubuted by Exeter Software (the biological softwarecompany, not the warehouse-inventory-software house of the same name).Their e-mail address is
sales(at) exetersoftware.com
. Theirtoll-free telephone number is 800-842-5892, their not-so-freephone number is +1-631-689-7838, and their fax number is +1-631-689-0103.Their mailing address is47 Route 25A, Suite 2, Setauket, NY 11733-2870 USA .Further information is available on theirWeb pageat http://www.exetersoftware.com/cat/ntsyspc/ntsyspc.html
.Warren Kovach of Kovach Computing Services, Anglesey,Wales (
info(at) kovcomp.co.uk
) has produced MVSP,a comprehensive multivariate statistical package for the PC platform.It can do many kinds of analyses (principal components, clustering, etc.)but the features relevant to this listing are clustering with a varietyof methods and a variety of distance measures, including Li and Nei'srestriction sites distance. MVSP may be ordered from Kovach Softwarethrough itsweb siteat http://www.kovcomp.com/mvsp/
.MVSP 3.1 for Windowscosts UK £85 or US$ 150 for an academic license.A version on CD with a printed manual is £20 ($35) more.Commercial licenses are £115 ($185).Version 2.2 for DOS costs UK £65 or US$ 100.Free evaluation versions which works for a limited period can bedownloaded from the Kovach Computing download web page athttp://www.kovcomp.co.uk/downl2.html#mvsp
. An evaluationversion of version 2.2 forDOS is also available for downloading by ftp fromgarbo.uwasa.fi
in directory pc/stat/
.MVSP is also distributed by Exeter Software atits web siteat http://www.ExeterSoftware.com/cat/kovach/mvsp.html
Version 3.1 costs $185 for an academic license, $265 for a commercial license.There are discounts for multi-user licenses.Other vendors include Rockware andGeoMem. János Podani of the Department of Plant Taxonomy and Ecology,Eötvös Loránd University, Budapest, Hungary (podani(at) ludens.elte.hu)has developed SYN-TAX 2000, a general package forclustering. It can calculate a wide variety of distance coefficients fromnumerical data, and can perform hierarchical clustering, nonhierarchicalclustering, and ordination. This includes, in addition to many clusteringmethods, minimum spanning trees and additive trees by Neighbor-Joining.SYN-TAX 2000 is available as commercial software from Exeter Software atits web site thereat
http://www.ExeterSoftware.com/cat/syntax/syntax.html
. It costs $350 for an educational license, $450 for a commerciallicense. Podani also maintains his own SYN-TAX web site at http://ramet.elte.hu/~podani/SYN2000.html
where there are descriptions, screen shots, some free upgrades ofcertain program components, and also an older DOS executableversion, 5.1, and a Macintosh version, SYN-TAX 5.02. There is a demoversion available for the DOS version, and both the DOS and Mac versionsare sold, each for $150 (for educational use $200), and both together for$300. Over the years various versions of SYN-TAX have been described by papers.The most recent description in a journal is: Podani, J. 1993. SYN-TAX 5.0: Computer programs for multivariate data analysis in ecology and systematics.Abstracta Botanica17: 289-302. John Archer and David Robertsonof the Faculty of Life Scienceof the University of Manchester, Manchester, UK(john.archer (at) postgrad.manchester.ac.uk)has produced CTreeversion 1.02, which is a tree viewing software with an emphasis of quantifying clusters present on tree topologies. CTree has been designed for the quantification of clusters within viral phylogenetic tree topologies.(it is not to be confused with the tree alignment programCtree).Clusters are stored as individual data structures from which statistical data, such as the Subtype Diversity Ratio (SDR), Subtype Diversity Variance (SDV) and pairwise distances can be extracted. Clusters can be selected manually or via a novel heuristic algorithm.Random trees can also be generated and used to generate control distributions of the various statistic data generated. Tree viewing features are also included along with output to PDF format.It is described in the paper:Archer, J., and D. L. Robertson. 2007. CTree: comparison of clusters betweenphylogenetic trees made easy. Bioinformatics23(21): 2952-2953.It is available as Java executables. It can be downloaded fromits web siteat
http://www.manchester.ac.uk/bioinformatics/ctree
B. McCune and M. J.Mefford of MjM Software,(mjm (at) centurytel.net)have released PC-ORD (PC Ordination),version 5.10, a package for clustering and ordination. It can do a varietyof kinds of clustering and ordination methods, including nonmetricmultidimensial scaling, principal coordinates analysis, and indicator speciesanalysis. For the purposes of this listing what is relevant is that itcan make dendrograms by clustering. This includes two-way clustering analysisthat clusters individuals as well as variables. These work directlyfrom a spreadsheet of data. I do not know what measures of distance ituses for this. The package is primarily intended for multivariate analysisof ecological data.It is available as Windows executables. It can be purchased and downloadedfromits web siteat
http://home.centurytel.net/~mjm/pcordwin.htm
.It is available at a price of $299 for a regular user, or $199 for a studentlicense. A license for each additional simultaneous user is $100 (or $50).Simon Goodman, then of the Institute of Cell, Animal, andPopulation Biology of the University of Edinburgh producedRSTCALC, version 2.2. It is primarilyintended to perform analyses of population structure, geneticdifferentiation and gene flow using microsatellite data.IT calculates estimates the Rst measure of differentiation among a number ofpopulations, but inaddition you can also use RSTCALC to obtain estimates of the delta-mu^2 distance measure. Its calculations are described in a paper:Goodman, S. J. 1997. Rst Calc: a collection of computer programs forcalculating estimates of genetic differentition from microsatellite data and a determining theirsignificance. Molecular Ecology6: 881-885. The program runs on Windows and is available fromits web site
http://www.biology.ed.ac.uk/research/institutes/evolution/software/rst/rst.html
as a Windows executable. Daniel Montagnon (Daniel.Montagnon (at)wanadoo.fr) of the Institut d'Embryologie, Faculté deMédecine, Strasbourg, France has writtenYCDMA (Y Chromosome Data MAnagement), version 1.2. This isa data management program for microsatellite data. It can do a wide varietyof management tasks, maintaining and manipulating databases of genotypes,calculating gene frequencies, and converting file formats.For the purposes of this listing, its relevant feature is the calculation ofa variety of gene frequency genetic distances between populations, anda squared copy number microsatellite genetic distance. YCDMA is written inMicrosoft Visual Basic. It is available as a Windows executable fromits web siteat
http://perso.wanadoo.fr/daniel.montagnon/YCDMAAng.htm
.Giorgio Bertorelle, of the Population Genetics and Genetic EpidemiologyGroup of the University of Ferrara, Italy (ggb(at) unife.it) hasreleased DIVAGE and DIVAGE_C. Theseprograms estimate the time of divergence of two populations based on thefrequencies of rare alleles in the two populations, where it is assumedthat these have each originated in a single mutational event before thedivergence of the populations. The two programs make differentassumptions about what is conditioned on what. The methods are described ina paper: Bertorelle, G. and B. Rannala. 1998. Using rare mutations to estimatepopulation divergence times: a maximum likelihood approach. Proceedings ofthe National Academy of Sciences, USA95: 15452-15457. The programs are DOS executables that will run in a Command Tool windowon Windows systems. They can be downloaded fromBertorelle's software web site at
http://web.unife.it/progetti/genetica/Giorgio/giorgio_soft.html
Stephane Guindon and Olivier Gascuelof the LIRMM (Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier)of the Université de Montpellier II, Montpellier, France(guindon (at) lirmm.fr and gascuel @ lirmm.fr)have released GAME (GAMma Estimation),version 1.0, a program to estimate the gamma parameter and use it to calculate distances and trees. GAME computes the optimal value of the gamma shape parameter (α). It uses a fast distance method based on BIONJ or FastME, which allows very large data sets (up to 1000 taxa) to be dealt with using a standard PC. It can use DNA or protein models and can analyze multiple data sets, such as result from bootstrapping. The value of α can either be inferred for all data sets separately, or just from the first data set.It is described in the paper:Guindon, S. and Gascuel, O. 2002. Efficient biased estimation of evolutionary distances when substitution rates vary across sites. Molecular Biology and Evolution19: 534-543.It is available as C source code, Windows executables, Linux executables and Powermac Mac OS X executables. It can be downloaded fromits web siteat
http://www.lirmm.fr/~guindon/gamma.html
It is also available as a web server here.Gaston Gonnet and Chantal Korostensky of theComputational Biochemistry Research Group at ETH inZürich, Switzerland, have made available Darwin,Data Analysis and Retrieval With IndexedNucleotide/peptide sequences,version 2.1.It is an environment which enables the user to carry out a variety ofkinds of analysis with sequences, including phylogeny methodsThese seem to include distance matrix, split decompositon,and a form of likelihood method. Darwin is availableas executables for Solaris, Intel-compatible Linux, Irix, andHP/Compaq/Digital Alpha machines. These are available free if the userregisters by filling out a form at the download page at the Darwinweb page. The executables can then be transferred to the user by ftpor by e-mail of encoded files. It is described in the paper:Gonnet, G. H., M. T. Hallett, C. Korostensky, and L. Bernardin. 2000.Darwin v. 2.0: an interpreted computer language for the biosciences.Bioinformatics16: 101-103.Details and distribution policies areexplained further atDarwin's web page at
http://cbrg.inf.ethz.ch/darwin
.Darwin is also made available asa server.Vladimir Makarenkov(makarenkov.vladimir (at) uqam.ca)of the Departement d'Informatique of theUniversité du Québec à Montréal andthe Département de Sciences Biologiques of theUniversité de Montréal, andPhilippe Casgrain
casgrain(at) magellan.umontreal.ca
) of theDépartement de Sciences Biologiques of theUniversité de Montréal have releasedT-REX (Tree and Reticulogram rEconstruXion), version 4.0a1.This program performs four methods of fitting an additive distance(distance in a nonclocklike tree) to a given dissimilarity. Themethods available include Sattath and Tversky's ADDTREE method,Nei and Saitou's Neighbor-Joining method, Gascuel's UNJ UnweightedNeighbor-Joining method, his BIONJ method, theCircular order reconstruction method of Makarenkov and Leclerc(1997), and Yushmanov (1984),and the MW weighted least-squares method by Makarenkov (1997) andMakarenkov and Leclerc (1998). A number of methods for fitting trees todistance matrices that have missing values are also available.Nucleotide sequence distance can be computed from sequences usingmany of the widely-used distances.The program can also carry out bootstrap and jackknife resampling toassess strength of support for features of the trees.It also allows construction and plottingof 'reticulograms' that show departures from treelike structure, andinteractive manipulation of the tree and reticulogram diagrams.It is described in the paper: Makarenkov, V. 2001. T-Rex: reconstructing andvisualizing phylogenetic trees and reticulation networks.Bioinformatics17: 664-668.Executables for Windows (the 4.0a1 version) and for Macintosh (the version1.2a4 executable for PowerMacs) and an executable for a 32-bit DOS versionare available atThe T-REX web site athttp://www.labunix.uqam.ca/~makarenv/trex.html
. C++ sourcecode is also available there. A webserver for T-REX with more tree construction and manipulation methods isalso available. Philippe Casgrain (casgrain (at) magellan.umontreal.ca) and Pierre Legendre (Pierre.Legendre (at) umontreal.ca), of theDépartement des Sciences Biologiques at the Université deMontréal have produced Permute! version 3.4 alpha 9,a program to do permutation tests of regression of variables. It canpermute distance matrices in a number of ways, one of which is to do soaccording to an ultrametric (clocklike) tree provided by the user. Theultrametric permutation method is described in these papers:
- Lapointe, F.-J., and P. Legendre. 1991. The generation of randomultrametric matrices representing dendrograms.Journal of Classification8: 177-200.
- Lapointe, F.-J. and P. Legendre. 1992. A statistical framework to test theconsensus among additive trees (cladograms). Systematic Biology41: 158-171.
http://www.bio.umontreal.ca/casgrain/en/labo/permute/index.html
Jérôme Goudet, of the Department of Ecology and Evolution of theUniversity of Lausanne, Switzerland (jerome.goudet(at) unil.ch)has written FSTAT, version 2.9.3.2, a program toestimate and test gene diversity statistics from codominant markers.For our purposes, the important feature is its ability to calculate theNei and Cockerham/Weir families of distance measures. It canconvert data in its own format to and from the format of Genepop.Version 2.9.2.3 is a Windows executable; an earlier version, 1.2, whichis a DOS executable is also available. Both can be downloadedfrom its web siteat
http://www2.unil.ch/popgen/softwares/fstat.htm
.Michel Raymond and François Roussetof the Equipe Génétique et Environnement of the Institut desSciences de l'Evolution at the University of Montellier II, France(Raymond (at) isem.univ-montp2.fr and Rousset (at) isem.univ-montp2.fr).have written distributed Genepop version 4.0,a program to carry out a variety of population genetics tests. It cantest assumptions of Hardy-Weinberg and linkage equilibrium,run log-likelihood G-based test of differentiation between populations,use Slatkin's rare allele method to estimate number of migrants per generation,and calculate allele frequencies. For our purposes the relevant feature isits ability to calculates Fst and Rst measures of population differentiation,which are genetic distances. It is described in a paper: Raymond, M. andF. Rousset. 1995. GENEPOP (version 1.2) population genetic software for exacttests and ecumenicism. Journal of Heredity86: 248-249.Genepop is a DOS executable that can run under Windows in a Command Toolwindow. It can be downloadedits web page at
http://kimura.univ-montp2.fr/~rousset/Genepop.htm
.An older version, 3.4, can be downloaded by ftp from the University ofMontpellier at ftp://ftp.cefe.cnrs.fr/PC/MSDOS/GENEPOP/
.A web server for Genepop 3.4 is also available in Australia at thethe John Curtin University of Technology.Laurent Excoffier of theComputational and Population Genetics Lab of the Institute of Zoology,University of Bern, Switzerland(laurent.excoffier(at) zoo.unibe.ch),Stephan Schneider, and David Roessli have releasedArlequin version 3.5.1, a program for population geneticsanalysis. It can perform many kinds of population genetic tasksincluding estimation of gene frequencies, testing of linkagedisequilibrium, and analysis of diversity between populations.For the purposes of this list, the relevant feature is its abilityto compute a variety of genetic distance measures includingof Jukes and Cantor, the Kimura2-parameter distance, and the Tamura-Nei distance, each of thesewith or without correction for gamma-distributed rates of evolution.It can also compute a Minimum Spanning Tree network.It is available as binaries for Windows, for either 32 or 64-bitprocessors. A special version to compute some summary statistics isalso included.An archive including the binaries and a PDF documentation file are available atits web siteat
http://cmpg.unibe.ch/software/arlequin3/
.Naoko Takezaki of the Life Science Research Centerof Kagawa University, Japan(
takezaki(at) med.kagawa-u.ac.jp
),Masastoshi Nei of the Institute of Molecular and Evolutionary Geneticsof the Department of Biology. Pennsylvania State University, University Park,Pennsylvania, and Koichiro Tamura of Tokyo Metropolitan University, Tokyo,Japanhave released POPTREE2, whichcomputes various genetic distance measures and constructstrees of populations or closely related species from genefrequency data by using the Neighbor-Joining method and UPGMA.POPTREE2 can compute Nei's genetic distance and his Dagenetic distance, as well as Latter's Fst* distance and the(Δμ)2 and Dsw measures of microsatellite genetic distance.It can also perform bootstrapping, and compute heterozygosity and Gst measures of the extent of genetic variation in a population and genetic differentiation among subdivided population.The program uses a Windows graphical user interface, andtrees can be displayed in a publishable for and changed by the user.POPTREE2 is described in a paper: Takezaki, N., M. Nei, and K. Tamura. 2009.POPTREE2: Software for constructing population trees from allele frequencydata and computing other population statistics with Windows interface.Molecular Biology and Evolution27: 747-752.It is available from its web siteat http://www.med.kagawa-u.ac.jp/~genomelb/takezaki/poptree2/index.html
.A source code Unix version (POPTREE version 1) and an executable DOS version (which is called poptrfdos) are also available there.It is also availablefrom the IUBIO archiveat http://iubio.bio.indiana.edu/soft/molbio/evolve
.POPTREE was also formerly called njbafd, andunder that name its earlier version is also available at the same IUBIO site.Olivier Hardy and Xavier Vekemans of the Service d'Eco-Ethologie Evolutiveat the the Université Libre de Bruxelles, Brussels, Belgium(ohardy (at) ulb.ac.be)distribute SPAGeDi(Spatial Pattern Analysis of Genetic Diversity),version 1.3, a program to compute a variety of different genetic diversity andgenetic distance statistics.It can compute various statistics describing relatedness or differentiationbetween individuals or populations by pairwise comparisons, and analyze howthese values are related to geographical distances in a way similar to aspatial autocorrelation analysis or by linear regression. The statisticscomputed include Fst, Rst, Ds (Nei's standardgenetic distance), and the microsatellite distance (delta mu)2 foranalyses at the population level and, for analyses at the individual level,pairwise kinship, relatedness and fraternity coefficients (with differentestimators for each) as well as Rousset's distance between individuals and akinship analogue based on allele size. It can also do bootstraps andpermutation analyses on the distances and geographic locations.It is available as Windows executables.It is described in the paper: Hardy, O. J. and X. Vekemans 2002. SPAGeDi: aversatile computer program to analyse spatial genetic structure at theindividual or population levels. Molecular Ecology Notes2:618-620. It can be downloaded from its web site at
It is distributed as a Windows executable fromits web siteat http://ebe.ulb.ac.be/ebe/Software.html
http://www.ub.es/dnasp/
.Jianzhi George Zhang, now of the Laboratory of Genomic and Molecular Evolutionin the Department of Ecology and Evolutionary Biology of the University ofMichigan, Ann Arbor, Michigan(jianzhi (at) umich.edu)wrote Bn-Bs, a programto estimate branch lengths in terms of synonymous and nonsynonymoussubstitutions per site, while the tree topology is given. The program uses themodified Nei-Gojobori method to estimate pairwisesynonymous and nonsynonymous distances among present-sequences and thenestimates branch lengths and their variances by using the ordinaryleast-squares method. The method is described in the paper:Zhang J., H. F. Rosenberg, and M. Nei. 1998. Positive Darwinian selectionafter gene duplication in primate ribonuclease genes. Proceedings of theNatonal Academy of Sciences, USA95: 3708-3713.It is available as C source code and as DOSexecutables from the software web site of Masatoshi Nei's lab inwhich the work was done. A zip archive of the files can be downloaded fromthe link there. A documentation file is can also be read there.Jianzhi George Zhang, now of the Laboratory of Genomic and Molecular Evolutionin the Department of Ecology and Evolutionary Biology of the University ofMichigan, Ann Arbor, Michigan(jianzhi (at) umich.edu)released HON-new, a program to compute the amounts ofconservative and radical amino acid substitution between pairs of DNAsequences of coding region exons. The program uses a classification ofamino acids into categories. Three types of amino acid classifications(by charge, by polarity and one of Miyata and Yasunaga) are provided. One can also define conservative and radical amino acid oneself.The method is modified from the original method ofHughes, Ota, and Nei (1990) by taking into account transition bias. It isdescribed in the paper: Zhang J. 2000. Rates of conservative and radicalnonsynonymous nucleotide substitutions in mammalian nuclear genes. Journalof Molecular Evolution50: 56-68. It is available in C sourcecode and as a Windows executable at the Nei laboratory software web site at
http://homes.bio.psu.edu/people/faculty/nei/software.htm
Kevin Thorntonof the Department of Ecology and Evolutionary Biologyof the University of California, Irvine, California(krthornton (at) uci.edu)has written analysisversion 0.7.3, a package to do population-genetic analyses of samples of DNA sequences. This is a package of programs to compute various tests and statistics on DNA sequence data within populations. For the purposes of this listing, the relevant feature is its ability to compute the Kimura K2P 2-parameter distance between sequences. It requires Thornton's libsequence C++ class library (available at the same site) and the GNU Scientific Library.The libsequence library is described in the paper: Thornton, K. 2003. libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics19(17): 2325-2327.It is available as C++ source code. It can be downloaded fromits web siteat
http://molpopgen.org/software/lseqsoftware.html
Daniel Montagnon (Daniel.Montagnon (at)wanadoo.fr) of the Institut d'Embryologie, Faculté deMédecine, Strasbourg, France has written NSA(Nucleotide Sequences Analyzer), version 3.3. It is a general programfor reading in sequences and writing them out in a variety of dataformats, with the ability to select particular sets of sites and sequences.For our purposes, the relevant feature is the ability to calculatea number of different nucleotide sequence distances, as well as somesimple protein sequence distances. These include the Jukes-Cantor,Kimura, and Tamura-Nei distances, as well as a simple protein distancebased on the fraction of similar amino acids. These can also have acorrection for a gamma distribution of rates across sites. The programis written in Visual Basic, and is available as a Windows executable fromits web siteat
http://perso.wanadoo.fr/daniel.montagnon/NSAAng.htm
John Brzustowski,of the Department of Biological Sciences of the University of Alberta, Canada(
jbrzusto(at) ualberta.ca
),wrote qclust, a program to carry out a number ofclustering methods including Neighbor-Joining. The neighbor-joining methodhas been improved over our own Neighbor program, so as to be able to handlelarge numbers of taxa much more quickly. The program is availablealong with another program, calcdist which calculatesdistances from 0/1 data. The programs are availableas C source and as DOS executables fromits webpage at http://www.biology.ualberta.ca/jbrzusto/dosclust.html
.A more interactive version of the program is also available as Java froma web pageat http://www2.biology.ualberta.ca/jbrzusto/cluster.php
.(Brzustowski has declared that both of these programs are unsupported software,and he will not answer questions about them). Keith Jolley, ofthe Epidemiology Group of the Department of Zoology, University of Oxford,Oxford, U.K. (keith.jolley (at) medawar.ox.ac.uk)has released S.T.A.R.T.2 (Sequence Type Analysis andRecombinational Tests), version 2. This is a set of tools forsumamrizing data, assigning lineages, and testing for recombination andselection. These are used with Multilocus Sequence Typing (MLST) data,which starts with DNA sequences at multiple loci, assigns alleles to eachsample at a number of loci and clustersstrains on the basis of the presence and absence of alleles. S.T.A.R.T.can calculate distances between strains based on these presences andabsences, and cluster strains by the UPGMA method. It can alsoassign strains to lineages, carry out several different tests forrecombination among strains, and do a pairwise dN/dS testing for selection.S.T.A.R.T.is described in a paper: Jolley K. A., E. J. Feil, M. S. Chan, and M. C.Maiden. 2001. Sequence type analysis and recombinational tests (START).Bioinformatics. 17: 1230-1231. It is available as a Windowsexecutable fromits web site at
http://pubmlst.org/software/analysis/start2/
. A previousversion, S.T.A.R.T., is available atanother page at the same web site. Joachim Friedrich, Thomas Dandekar, Matthias Wolf,and Tobias Müller, of the Department of Bioinformatics, Biocenter,University of Würzburg, Germany (ProfDist (at) biozentrum.uni-wuerzburg.de> have written ProfDist, version 0.9.8, a program for constructing large trees fromprofile distances of nucleotide sequences. Given a number of clades andDNA or RNA sequences, it constructs a profile for each clade, computes profile distances among these, and uses Profile NeighborJoining (PNJ) to compute a tree.ProfDist is described in the paper: Müller, T., S. Rahmann, T. Dandekar,and M. Wolf. 2004. Accurate and robust phylogeny estimation based on profiledistances: a study of the Chlorophyceae (Chlorophyta).BMC Evolutionary Biology4: 20.ProfDist is available as a Windows executable, or as source codefor Windows, Linux, or Mac OS X. It is distributed from its web site at
http://profdist.bioapps.biozentrum.uni-wuerzburg.de/
.Olivier Langella (
Olivier.Langella(at) pge.cnrs-gif.fr
)of the Laboratoire PGE, CNRS UPR9034, Gif sur Yvette, France, distributesPopulations, version 1.2.30. It can calculate a widevariety of distances from multiple-allele diploid or haploid genotypesand from microsatellite data, and canalso infer phylogenies by distance methods including Neighbor-Joining andUPGMA. It can bootstrap the data across loci and/or across individuals when constructing phylogenies. The trees can be trees of populations ortrees of individuals.Populations is available as a free download from its web site at http://bioinformatics.org/~tryphon/populations/
, as source code, as executables for Windows. Patrick Meirmansof the Department of Ecology and Evolutionof the University of Lausanne, Switzerland(patrick.meirmans (at) unil.ch)has written GenoDive(Genotypic Diversity), version 2b9, a program for population genetic analyses. It can do Analysis Of Molecular VAriance, estimation ofstandardised coefficients of population differentiation, k-means clustering ofpopulations using a simulated annealing approach, assigning genotypic identity(clones) to individuals, testing for clonal reproduction, testingHardy-Weinberg equilibrium, calculation of the hybrid index for individuals,and different types of Mantel tests. The distances that it cancompute are the features relevant to this listing. It can handle genetic data as well as distance matrices and ecological data, enabling you to combine data from several different sources into a single analysis.It is described in the paper:Meirmans, P. G. and P.H. Van Tienderen. 2004. GENOTYPE and GENODIVE: twoprograms for the analysis of genetic diversity of asexual organisms.Molecular Ecology Notes4: 792-794.It is available as Mac OS X universal executables. It can be downloaded fromits web siteat
http://www.bentleydrummer.nl/software
Allen Rodrigo, Alexei Drummond, and Matthew Goode of theComputational and Evolutionary Biology Laboratory, School of BiologicalSciences, University of Auckland, New Zealand(a.rodrigo(at) auckland.ac.nz and m.goode (at) auckland.ac.nz) have releasedPebble, version 1.0,(Phylogenetics, Evolutionary Biology, and Bioinformatics in a moduLarEnvironment)This is a graphical user interface around a functional programming languagefor evolutionary inferences. The system is written in Javausing the PAL project classes asits components. This alpharelease provides the basic user interface and some component packages.The following analyses and tools are available in vCEBL 0.3a:
- Construction of serial sample phylogenies using sUPGMA or sWPGMA withsampling times known exactly or ordinally.
- Construction of Neighbor-Joining, UPGMA and WPGMA phylogenies.
- Estimation of pairwise distance matrices using user-specified ratematrices (but not yet allowing variation of rates between sites).
- Estimation of population parameters including substitution/mutation ratesusing pairwise distances with or without parametric bootstrap confidenceintervals.
- Maximum-likelihood branch-length optimization of user-specifiedtree, including serial sampled clocklike trees.
- ML estimation of divergence between serial samples assuming constant orvarying mutation rates.
- Simulation of genealogies and sequences under a constant-sized populationmodel with or without serial sampling.
http://www.cebl.auckland.ac.nz/software2.php
. It requiresJava VM 1.1.1 or higher. It can also be obtained there as an applet for yourbrowser, with some features lacking.Phylip software, free download Windows 10
Le Sy Vinh (Vinh (at) cs.uni-duesseldorf.de) of the Bioinformatics Institute of the University ofDüsseldorf, Germany and Arndt von Haeseler(arndt.von.haeseler (at) univie.ac.at)of the Centre for Integrative Bioinformatics Vienna (CBIV)have released STC (Shortest Triplet Clustering). This methodconstructs k-representative sets from triplet of species. The resulingclustering method is O(n2) in speed and can handle thousands ofspecies with good accuracy. It is described in a paper: Vinh, L. S. and A.von Haeseler. 2005. Shortest triplet clustering: reconstructing largephylogenies using representative sets. BMC Bioinformatics6:92. The program is available as Linux and as Windows executables atits web site at
http://www.cibiv.at/software/stc/
Naoko Takezaki of the Life Science Research Center of Kagawa University,Japan (
takezaki(at) med.kagawa-u.ac.jp
) has written sendbs.It computes average nucleotide substitutions within and between populations. Themethod is described in the paper by M. Nei and L. Jin (1989, MolecularBiology and Evolution6: 290-300). However, sendbs differs fromtheir method by using a bootstrap across sites obtain standard errors ofthe distances.It also constructs a tree of populations using a neighbor-joining method. It is distributed as source code for Unix, and also as a DOS executable, fromby ftp from the Indiana ftp serverand through the software page of Masatoshi Nei's labat Pennsylvania State University athttp://www.bio.psu.edu/People/Faculty/Nei/Lab/software.htm
.Applied Maths BVBA of Keistraat 120, 9830 Sint-Martens-Latem, Belgium has released GelCompar II, acomprehensive 1-d gel analysis program. It includes capabilities ofclustering data taken from the gels. These are described as 'includingphylogenetic and dimensioning algorithms'. The phylogenyalgorithms include a number of distance-matrix clustering methods.It is also said to be able to carry out generalized parsimony.Gelcompar II is a Windows program. It is describedat its web site at
http://www.applied-maths.com/gc/gc.htm
. A detailedbrochure is available for downloading there. Gelcompar II is commercialsoftware. For price and ordering information contact them by phone at +32 9 22222 100, fax them at +32 9 2222 102, e-mail them atinfo(at) applied-maths.com, or use the information request form attheir web pages. Their U.S. Sales Office is at Applied Maths Inc.,512 East 11th Street, Suite 207, Austin, Texas 78701. phone +1 512-482-9700, fax +1 512-482-9708 (email is info-us(at) applied-maths.com). (One company vending Gelcompar II sells the wholepackage for $20,000, though if only the basic module and the cluster analysismodule are ordered the price is $5,400).Andrey Rzhetsky, now of the Department of Human Genetics at the University ofChicago (arzhetsk (at) medicine.bsd.uchicago.edu)Statio, a program for testing stationarity of nucleotidecomposition or amino acid composition in pairs of sequences. The program readsa pair of sequences and then tests stationarity under a number of possiblemodels of DNA evolution or protein evolution. The method is described ina paper: Rzhetsky, A. and M. Nei. 1994. Tests of applicability of several substitution models for DNA sequence data. Molecular Biology and Evolution12(1): 131-151.It can be downloaded as a setof MSDOS executables from the Nei lab software web siteat
https://homes.bio.psu.edu/people/faculty/nei/software.htm
.Probal Chaudhuriof the Theoretical Statistics and Mathematics Divisionof the Indian Statistical Institute, Calcutta, India(probal (at) isical.ac.in)has released SWORDS(Statistical analysis of WORDS in DNA sequences),a package for analyzeingthe frequencies and distribution of DNA words(subsequences) in multiple species. It has programs for drawing frequencycurves and star plots of DNA wonds of given size. It can calculate distancematrices, infer phylogenies by UPGMA clustering.It also estimates the bootstrap values for the phylogenetic tress. It alsocan analyze position of the sequences and do other descriptive statisticsand tests. As it does not need aligned sequences, SWORDS canhandle large genome sizes. The methods and the program are described in thepapers:
- Chaudhuri, P. and S. Das. 2001. Statistical analysis of large DNA sequences using distribution of DNA words. Current Science80 1161-1166.
- Chaudhuri, P. and S. Das. 2002. SWORDS : a statistical tool for analyzing large DNA sequences. Journal of Biosciences27: 1-6.
Phylip software, free download Windows 8
http://www.isical.ac.in/~probal/main.htm
. It is described asavailable as C++ source code, Windows executables, Linux executables andMac OS X universal executables.Mike Sanderson (sanderm(at) email.arizona.edu)of Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona has writtenr8s, version 1.71, a program to adjust branch lengths and divergencetimes in a phylogeny to infer divergence times by smoothing rates of evolutionto approximate a molecular clock (allow a 'relaxed' clock). The programis given the tree with branch lengths as input and smooths this tree andinfers divergence times. Sanderson's main approaches to smoothing divergencetimes are described in his papers:
- Sanderson, M. J. 1997. A nonparametric approach to estimating divergencetimes in the absence of rate constancy. Molecular Biology and Evolution14: 1218-1231.
- Sanderson, M. J. 2002. Estimating absolute rates of molecular evolutionand divergence times: a penalized likelihood approach.Molecular Biology and Evolution19: 101-109.
http://loco.biosci.arizona.edu/r8s/index.html
.Torsten Eriksson of the Bergius BotanicalGarden, Stockholm, Sweden (
torsten(at) bergianska.se
)has released the r8s bootstrap kit. This is a numberof Perl scripts and three general command blocks for PAUP* and r8s which enable bootstrappinganalyses with r8s. It is available from hissoftware web siteat http://www.bergianska.se/index_forskning_soft.html
.Phylip software, free download Camtasia
Kai Chan (kaichan(at) stanford.edu)of the Department of Biological Sciences, Stanford University, Stanford,California, and Brian Moore(brian.moore(at) yale.edu) of the Department of Ecology andEvolutionary Biology, Yale University, New Haven, Connecticuthave released SymmeTREE version 1.1. It is a programto test whether branches of a tree have diversified at different rates,and along which branches the significant shifts of diversity have occurred.This is evaluated using the species diversity of different parts of the tree.The program is described in a paper: Chan, K. M. A. and B. R. Moore. 2004.SYMMETREE: whole-tree analysis of differential diversification rates.Bioinformatics Advance Access publication November 30, 2004.The program is available as executables for Windows, Mac OS X, and Linuxand as source code for other flavors of Unix. It is distributed fromits web site at
http://www.phylodiversity.net/bmoore/software.html
.Phylip software, free download Version
Galina Glazko, now of the Department of Biomedical Informatics of the University ofArkansas Medical School, Little Rock, Arkansas(GVGlazko (at) uams.edu) andMasatoshi Nei of the Institute of Molecular Evolutionary Genetics atPennsylvania State University, University Park, Pennsylvania have releasedTIMER, which estimates divergence times using a linearizedtree approach. It can use DNA or protein sequences at multiple loci. Itconstructs a phylogeny using the Neighbor-Joining method, and then estimatesbranch lengths and divergenece times for the individual loci as well as for thefull set of loci. It can carry out the Two-Cluster Test for constancy ofrate of divergence at an individual node in the tree. The methods areexplained in a paper: Nei, M., P. Xu, and G. Glazko. 2001. Estimation ofdivergence times from multiprotein sequences for a few mammalian species andseveral distantly related organisms. Proceedings of the National Academy ofSciences98: 2497-2502. TIMER is available as a Windows executableat the Nei lab software web siteat
https://homes.bio.psu.edu/people/faculty/nei/software.htm
Phylip software, free download Mac
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