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.
| Software | Version | Description | Home page | Platform |
| Arlequin | 2001 | Arlequin 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.php | Web |
| Big Heap - SeeHeapbelow | ||||
| Bottleneck | 1.2.02 | Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies | http://www.montpellier.inra.fr/URLB/bottleneck/bottleneck.html | Win |
| BoxShade | 3.2.1 | Pretty Printing and Shading of Multiple-Alignment files | http://www.ch.embnet.org/software/BOX_form.html | Web |
| Cervus | 2.0 | CERVUS 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.html | Win |
| ClustalW | - | Multiple sequence alignments | http://www2.ebi.ac.uk/clustalw/ | Web |
| ClustalX | 1.83 | Multiple sequence alignments (stand-alone versions) | ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/ | Mac, Win, Unix |
| Component | 2.0 | Tree comparison software | http://taxonomy.zoology.gla.ac.uk/rod/cpw.html | Win |
| DAMBE | Sep 5 2002 | DAMBE is an integrated software package for retrieving, converting, manipulating, aligning and analyzing molecular sequence data. | http://aix1.uottawa.ca/~xxia/software/software.htm | Win |
| Dialign | 2.2.1 | A novel algorithm for pairwise as well as multiple alignment of nucleic acid and protein sequences | http://bibiserv.techfak.uni-bielefeld.de/dialign/ | Web |
| DnaSP | 3.5.3 | A software package for the analysis of nucleotide polymorphism from aligned DNA sequence data | http://www.ub.es/dnasp/ | Win |
| EasyPOP | 1.8 | Easypop is intended to simulate population genetics datasets under a very broad range of conditions | http://www.unil.ch/izea/softwares/easypop.html | Mac, 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.htm | Mac, Win |
| FStat | 2.9.3.2 | FSTAT 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.html | Win |
| GDA | 1.1 | GDA (Genetic Data Analysis) is a Microsoft Windows program for analyzing discrete genetic data | http://lewis.eeb.uconn.edu/lewishome/software.html | Win |
| GeneClass | 2 | GeneClass is a program for assignation and exclusion using molecular markers | http://www.montpellier.inra.fr/CBGP/softwares | Win, Linux |
| GeneDoc | 2.6.02 | A 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. | ||||
| GenePop | 3.3 | GENEPOP 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.html | Web | |
| Genetic Studio - This software appears to no longer be available from the author's web site. | ||||
| Genetix | 4.04 | This set of programs computes several basic parameters of population genetics | http://www.univ-montp2.fr/~genetix/genetix/genetix.htm | Win |
| GeneTree | 1.3.0 | GeneTree is an experimental program for comparing gene and species trees | http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html | Mac, Win |
| GeoDis | 2.0 | A program for the Cladistic Nested Analysis of the Geographical Distribution of Genetic Haplotypes | http://zoology.byu.edu/crandall_lab/geodis.htm | Java |
| 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.htm | Mac, Win |
| Kinship | 1.3.1 | Kinship is a program to perform maximum likelihood tests of pedigree relationships between pairs of individuals in a population | http://www.gsoftnet.us/GSoft.html | Mac |
| LAMARC | 1.1 | LAMARC 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.html | Mac, 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 |
| LVB | 1.0a / 2.0b2 | Reconstructing evolution with parsimony and simulated annealing | http://www.rubic.reading.ac.uk/lvb/ | Mac, Win, Unix |
| MacClade | 4.05 | MacClade 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.html | Mac |
| MantelStruct | ?? | A Windows™ program for the detection of population structure via mantel tests. | http://bioweb.usu.edu/mpmbio/_vti_bin/shtml.dll/mantel.htm | Win |
| MEGA | 2.1 | Molecular Evolutionary Genetics Analysis | http://www.megasoftware.net/text/overview.sht | Win |
| MinSpNet | ?? | Computes a minimum spanning network among a set of OTUs | http://lgb.unige.ch/software/win/min-span-net/ | Win |
| ModelTest | 3.06 | Modeltest 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.htm | Mac, Win, Unix |
| MolEco - The software appears no longer to be available from the author's web page. | ||||
| MrBayes | 3.0 | Program for Bayesian inference of phylogenies | http://morphbank.ebc.uu.se/mrbayes/ | Mac, Win, Unix |
| NDE | 0.5.0 | A Nexus Data Editor for Windows | http://taxonomy.zoology.gla.ac.uk/rod/NDE/nde.html | Win |
| PAML | 3.13 | PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood | http://abacus.gene.ucl.ac.uk/software/paml.html | Mac, Win, Unix |
| PAUP* | 4.0b10 | Tools for inferring and interpreting Phylogenetic trees | http://paup.csit.fsu.edu/index.html | Mac, Win, Dos, Unix |
| PCAGen | 1.2.1 | PCAGEN is a computer package for windows which perform Principal Component Analysis (PCA) on gene frequency data | http://www.unil.ch/izea/softwares/pcagen.html | Win |
| Phylip | 3.6a3 | Free software for inferring phylogenies | http://evolution.genetics.washington.edu/phylip.html | Mac, Win, Unix |
| PopGene | 1.32 | A 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 |
| ProSeq | 2.9 | ProSeq is a Win95 program for sequence editing and population genetics (mol/evol) analysis. | http://helios.bto.ed.ac.uk/evolgen/filatov/proseq.html | Win |
| PRT | 1.2 | A software toolbox for pedigree reconstruction based on DNA marker input | http://ace.acadiau.ca/~aalmudev/pedigree.htm | Win |
| Puzzle - NB. Has now been renamed Tree-Puzzle: See below | ||||
| RadCon | 1.1.5 | RadCon is a free phylogenetic tree consensus and comparison program, for the MacOS | http://darwin.zoology.gla.ac.uk/~jthorley/radcon/radcon.html | Mac |
| Relatedness | 5.08 | Relatedness calculates average genetic relatedness among sets of individuals defined by demographic variables, either on average or by pairs. | http://www.gsoftnet.us/GSoft.html | Mac |
| RSTCALC | 2.2 | RSTCALC 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.html | Win |
| SITES | ?? | SITES is a computer program for the analysis of comparative DNA sequence data. | http://lifesci.rutgers.edu/~heylab/DistributedProgramsandData.htm | Mac, Win |
| Spectrum | 2.3.0d | SpectrumTM 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.html | Mac, Win |
| STRand | 20030520 | STRand 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.htm | Win |
| TreeMap | 2.02b | TreeMap is an experimental program for comparing host and parasite trees | http://taxonomy.zoology.gla.ac.uk/rod/treemap.html | Mac, Win |
| TreeView | 1.6.6 | TreeView is a simple program for displaying phylogenies. | http://taxonomy.zoology.gla.ac.uk/rod/treeview.html | Mac, Win, Unix |
| Tree Puzzle | 5.1 | TREE-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.htm | Mac, Win |
| WinClada | 0.9.99m24 | A windows program for creating, editing, and analyzing systematic data sets. | http://www.cladistics.com/about_winc.htm | Win |