Genetic Analysis Software Links

Following the February 2002 INSECTS workshop in Oulu, I have added links to various Genetic Analysis software packages. Please let me know if there are any errors, omissions or broken links in the following list. Also let me know if you'd like to see the list organised in a different way.

Descriptions are mostly culled from the first line of the description of the program on its home page, and may or may not give an accurate description of what the program does.

The "platform" column gives some indication of which hardware platform the programs can utilise, but this does not mean that they will run successfully on your particular version of the operating system! (eg. several programs do not run under Windows XP, although they are written for eg.Windows 95; many do not run on Windows 3.1). Java programs should run on most hardware platforms with a suitable "Java virtual machine". Web programs allow input of data and retrieval of results through a web browser.

At the moment I've made no distinction in this list between Freeware, Shareware and Commercial software, so don't blame me if you can't use the software you want on licensing grounds.

This list was last checked and updated on 9 June 2003.

SoftwareVersionDescriptionHome pagePlatform
Arlequin2001Arlequin is an exploratory population genetics software environment http://lgb.unige.ch/arlequin/Java
Assigment-Takes genotypes of individuals from several populations and determines from which population each individual is most likely to have come. http://www.biology.ualberta.ca/jbrzusto/Doh.phpWeb
Big Heap - SeeHeapbelow
Bottleneck1.2.02Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies http://www.montpellier.inra.fr/URLB/bottleneck/bottleneck.htmlWin
BoxShade3.2.1Pretty Printing and Shading of Multiple-Alignment files http://www.ch.embnet.org/software/BOX_form.htmlWeb
Cervus2.0CERVUS is a Windows 95-based program designed for large-scale parentage analysis using co-dominant loci. http://helios.bto.ed.ac.uk/evolgen/cervus/cervus.htmlWin
ClustalW-Multiple sequence alignments http://www2.ebi.ac.uk/clustalw/Web
ClustalX1.83Multiple sequence alignments (stand-alone versions) ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/ Mac, Win, Unix
Component2.0Tree comparison software http://taxonomy.zoology.gla.ac.uk/rod/cpw.htmlWin
DAMBESep 5 2002DAMBE is an integrated software package for retrieving, converting, manipulating, aligning and analyzing molecular sequence data. http://aix1.uottawa.ca/~xxia/software/software.htmWin
Dialign2.2.1A novel algorithm for pairwise as well as multiple alignment of nucleic acid and protein sequences http://bibiserv.techfak.uni-bielefeld.de/dialign/Web
DnaSP3.5.3A software package for the analysis of nucleotide polymorphism from aligned DNA sequence data http://www.ub.es/dnasp/Win
EasyPOP1.8Easypop is intended to simulate population genetics datasets under a very broad range of conditions http://www.unil.ch/izea/softwares/easypop.htmlMac, Win
FPG??FPG (Forward Population Genetic simulation) simulates a population of constant size that is undergoing various evolutionary processes, including: mutation, recombination, natural selection, and migration. http://lifesci.rutgers.edu/~heylab/DistributedProgramsandData.htmMac, Win
FStat2.9.3.2FSTAT is a computer package for PCs which estimates and tests gene diversities and differentiation statistics from codominant genetic markers http://www.unil.ch/izea/softwares/fstat.htmlWin
GDA1.1GDA (Genetic Data Analysis) is a Microsoft Windows program for analyzing discrete genetic data http://lewis.eeb.uconn.edu/lewishome/software.htmlWin
GeneClass2GeneClass is a program for assignation and exclusion using molecular markers http://www.montpellier.inra.fr/CBGP/softwaresWin, Linux
GeneDoc2.6.02A Full Featured Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows http://www.psc.edu/biomed/genedoc/Win
GeneLoss - This software appears to no longer be available from the author's web site.
GenePop3.3GENEPOP is a population genetic software package, able to computes exact tests and estimates of classical population parameters. ftp://ftp.cefe.cnrs-mop.fr/genepop/Win
GenePop (Web version)- http://wbiomed.curtin.edu.au/genepop/index.htmlWeb
Genetic Studio - This software appears to no longer be available from the author's web site.
Genetix4.04This set of programs computes several basic parameters of population genetics http://www.univ-montp2.fr/~genetix/genetix/genetix.htmWin
GeneTree1.3.0GeneTree is an experimental program for comparing gene and species trees http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.htmlMac, Win
GeoDis2.0A program for the Cladistic Nested Analysis of the Geographical Distribution of Genetic Haplotypes http://zoology.byu.edu/crandall_lab/geodis.htmJava
Heap??The program sucks in text files of DNA sequence, and performs a number of handy analyses and operations http://www.oeb.harvard.edu/palumbi/HEAP/Mac
HKA??HKA is a computer program that carries out the widely used statistical test for natural selection that was developed by Hudson, Kreitman and Aguadé. http://lifesci.rutgers.edu/~heylab/DistributedProgramsandData.htmMac, Win
Kinship1.3.1Kinship is a program to perform maximum likelihood tests of pedigree relationships between pairs of individuals in a population http://www.gsoftnet.us/GSoft.htmlMac
LAMARC1.1LAMARC is a package of programs for computing population parameters, such as population size, population growth rate and migration rates by using likelihoods for samples of data from populations. http://evolution.genetics.washington.edu/lamarc.htmlMac, Win, Unix
LAPD??This program allows to estimate maximum likelihood allele and two-locus haplotype frequencies, using an Expectation-Maximization algorithm, taking into account family relationships of the individuals. http://lgb.unige.ch/software/win/lapd/Win
LVB1.0a / 2.0b2Reconstructing evolution with parsimony and simulated annealing http://www.rubic.reading.ac.uk/lvb/Mac, Win, Unix
MacClade4.05MacClade is a computer program for phylogenetic analysis. Its analytical strength is in studies of character evolution. It also provides many tools for entering and editing data and phylogenies, and for producing tree diagrams and charts. http://phylogeny.arizona.edu/macclade/macclade.htmlMac
MantelStruct??A Windows™ program for the detection of population structure via mantel tests. http://bioweb.usu.edu/mpmbio/_vti_bin/shtml.dll/mantel.htmWin
MEGA2.1Molecular Evolutionary Genetics Analysis http://www.megasoftware.net/text/overview.shtWin
MinSpNet??Computes a minimum spanning network among a set of OTUs http://lgb.unige.ch/software/win/min-span-net/Win
ModelTest3.06Modeltest helps a user to choose the model of DNA substitution that best fits his/her data, among 56 possible models. This is accomplished through an implementation of hierarchical likelihood ratio tests and the AIC criterion http://zoology.byu.edu/crandall_lab/modeltest.htmMac, Win, Unix
MolEco - The software appears no longer to be available from the author's web page.
MrBayes3.0Program for Bayesian inference of phylogenies http://morphbank.ebc.uu.se/mrbayes/Mac, Win, Unix
NDE0.5.0A Nexus Data Editor for Windows http://taxonomy.zoology.gla.ac.uk/rod/NDE/nde.htmlWin
PAML3.13PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood http://abacus.gene.ucl.ac.uk/software/paml.htmlMac, Win, Unix
PAUP*4.0b10Tools for inferring and interpreting Phylogenetic trees http://paup.csit.fsu.edu/index.htmlMac, Win, Dos, Unix
PCAGen1.2.1PCAGEN is a computer package for windows which perform Principal Component Analysis (PCA) on gene frequency data http://www.unil.ch/izea/softwares/pcagen.htmlWin
Phylip3.6a3Free software for inferring phylogenies http://evolution.genetics.washington.edu/phylip.htmlMac, Win, Unix
PopGene1.32A user-friendly computer freeware for the analysis of genetic variation among and within populations using co-dominant and dominant markers http://www.ualberta.ca/~fyeh/Win
ProSeq2.9ProSeq is a Win95 program for sequence editing and population genetics (mol/evol) analysis. http://helios.bto.ed.ac.uk/evolgen/filatov/proseq.htmlWin
PRT1.2A software toolbox for pedigree reconstruction based on DNA marker input http://ace.acadiau.ca/~aalmudev/pedigree.htmWin
Puzzle - NB. Has now been renamed Tree-Puzzle: See below
RadCon1.1.5RadCon is a free phylogenetic tree consensus and comparison program, for the MacOS http://darwin.zoology.gla.ac.uk/~jthorley/radcon/radcon.htmlMac
Relatedness5.08Relatedness calculates average genetic relatedness among sets of individuals defined by demographic variables, either on average or by pairs. http://www.gsoftnet.us/GSoft.htmlMac
RSTCALC2.2RSTCALC is a PC-based program for performing analyses of population structure, genetic differentiation and gene flow using microsatellite data. http://helios.bto.ed.ac.uk/evolgen/rst/rst.htmlWin
SITES??SITES is a computer program for the analysis of comparative DNA sequence data. http://lifesci.rutgers.edu/~heylab/DistributedProgramsandData.htmMac, Win
Spectrum2.3.0dSpectrumTM is a Macintosh® program designed to read in a data file comprising aligned character arrays (such as DNA sequence data) or distance data in the form of a matrix, and perform some simple spectral analysis procedures on that data http://taxonomy.zoology.gla.ac.uk/~mac/spectrum/spectrum.htmlMac, Win
STRand20030520STRand can automate or speed up the analysis of DNA fragment length polymorphism samples run on fluorescence based gels. http://www.vgl.ucdavis.edu/STRand/Win
TFPGA??A Windows program for the analysis of allozyme and molecular population genetic data. http://bioweb.usu.edu/mpmbio/index.htmWin
TreeMap2.02bTreeMap is an experimental program for comparing host and parasite trees http://taxonomy.zoology.gla.ac.uk/rod/treemap.html Mac, Win
TreeView1.6.6TreeView is a simple program for displaying phylogenies. http://taxonomy.zoology.gla.ac.uk/rod/treeview.htmlMac, Win, Unix
Tree Puzzle5.1TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood http://www.tree-puzzle.de/Mac, Win, Unix
WH??WH is a computer program that carries out the fitting of the speciation model of Wakeley and Hey. http://lifesci.rutgers.edu/~heylab/DistributedProgramsandData.htmMac, Win
WinClada0.9.99m24A windows program for creating, editing, and analyzing systematic data sets. http://www.cladistics.com/about_winc.htmWin

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