Genetic Software List

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Detailed description of software

Admix

Web address: http://web.unife.it/progetti/genetica/Isabelle/admix2_0.html

Description: computes admixture proportions from molecular data

References:
Bertorelle G., Excoffier L. 1998. Inferring admixture proportions from molecular data. Molecular Biology and Evolution 15:1298-1311.
Dupanloup I., Bertorelle G. 2001. Inferring admixture proportions from molecular data: extension to any number of parental populations. Molecular Biology and Evolution 18: 672-675.

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Arlequin

Web address: http://anthro.unige.ch/arlequin/

Description: does many kinds of analyses for many kinds of molecular data (RFLPs, AFLPs, minisatellites, sequences, microsatellites, allozymes et al.)

Reference: Schneider S, Roessli D, Excoffier L. 2000. Arlequin ver. 2.000: A software for population genetics data analysis. Genetics and Biometry Laboratory, Univesity of Geneva, Switzerland.

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BOTTLENECK

Web address: http://www.ensam.inra.fr/URLB/bottleneck/bottleneck.html

Description: detection of recent effective population size reductions from allele data frequencies

Reference: Cornuet J.M. and Luikart G. 1997. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001-2014.

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CERVUS

Web address: http://helios.bto.ed.ac.uk/evolgen/cervus/cervus.html

Description: CERVUS is a Windows 95-based program designed for large-scale parentage analysis using co-dominant loci. Analysis is broken down into three sequential stages. Using genotype data in text file format, the program can analyse allele frequencies, run appropriate simulations and carry out likelihood-based parentage analysis, testing the confidence of each parentage using the results of the simulation. Simulations may also be used to estimate the power of a series of loci for parentage analysis, using real or imaginary allele frequencies.

Reference: Marshall T.C., Slate J., Kruuk L., Pemberton J.M. 1998. Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology 7: 639-655.

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DOH

Web address: http://www2.biology.ualberta.ca/jbrzusto/Doh.php

Description: takes genotypes of individuals from several populations and determines from which population each individual is most likely to have come, by using the assignment index, the highest probability of an individual's genotype in any of the populations.

References:
Paetkau D., Calvert W., Sterling I., Strobeck. C. 1995. Microsatellite analysis of population structure in Canadian polar bears. Molecular Ecology 4:347-354
Paetkau D., Waits L. P., Clarkson P. L., Craighead L., Strobeck C.. 1997. An empirical evaluation of genetic distance statistics using microsatellite data from bear (Ursidae) populations. Genetics 147:1943-1957

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FSTAT

Web address: http://www.unil.ch/izea/softwares/fstat.html

Description: estimates and tests gene diversities and differentiation statistics f rom codominant genetic markers; computes both Nei and Weir & Cockerham families of estimators of gene diversities and F-statistics, and tests them using randomisation methods

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GDA

Web address: http://newfish.mbl.edu/Course/Software/GDA/

Description: GDA is a program for analyzing allelic data. It can be used to calculate basic descriptive statistics, Wright's F-statistics, genetic distance matrices, and exact disequilibrium tests.

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GENECLASS

Web address: http://www.ensam.inra.fr/URLB/geneclass/geneclass.html

Description: assignation and exclusion using molecular markers

Reference: Cornuet JM, Piry S, Luikart G, Estoup A. 1999. New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153:1989-2000.

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GENEPOP

Web address: ftp://ftp.cefe.cnrs-mop.fr/genepop/

Description: GENEPOP is a population genetic software package, able to perform three major tasks.
It computes exact tests: for Hardy-Weinberg equilibrium, for population differentiation and for genotypic disequilibrium among pairs of loci.
It computes estimates of classical population parameters, such as Fst and other correlations, allele frequencies, etc.
It converts the input GENEPOP file to formats used by other programs, like Biosys (Swofford and Selander, 1981), Fstat (Goudet, 1995) and Linkdos (Garnier-Gere and Dillmann, 1992). Linkdos is also provided with GENEPOP, with the authorization of their authors. Slatkin’s isolation-by-distance program, DIST, available in previous versions of Genepop, has been replaced by the program ISOLDE (included in this version).

Includes tests from the following references:
Garnier-Gere P and Dillmann C, 1992. A computer program for testing pairwise linkage disequilibria in subdivided populations. J Heredity 83:239.
Goudet J, Raymond M, De Meeüs T and Rousset F, 1996. Testing differentiation in diploid populations. Genetics 144:1933-1940.
Raymond M and Rousset F, 1995. An exact test for population differentiation. Evolution 49 :1280-1283.
Rousset F and Raymond M, 1995. Testing heterozygote excess and deficiency. Genetics 140 :1413-1419.
Rousset F, 1996. Equilibrium values of measure of population subdivision for stepwise mutation processes. Genetics 142 :1357-1362.
Rousset F, 1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145 : 1219-1228.

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GENETIX

Web address: http://www.univ-montp2.fr/%7Egenetix/genetix/genetix.htm

Description: computes several basic parameters of population genetics such as Nei's D and H, Wright's F-statistics (the Weir-Cockerham's and Robertson-Hill's estimators), and linkage disequilibrium D according to Black & Krafsur.

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IMMANC

Web address: http://www.rannala.org/docs/immanc.html

Description: program designed to test whether or not an individual is an immigrant or is of recent immigrant ancestry.

Reference: Rannala B. Mountain J.L. 1997. Detecting immigration by using multilocus genotypes. PNAS USA 94: 9197-9201

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Kinship

Web address: http://www.bioc.rice.edu/Keck2.0/labs/

Description: performs maximum likelihood tests of pedigree relationships between pairs of individuals in a population

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MICROSAT

Web address: http://hpgl.stanford.edu/projects/microsat/

Description: does many microsatellite distance analyses

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Migrate

Web address: http://evolution.genetics.washington.edu/lamarc/migrate.html

Description: estimates migration rates and effective population numbers; takes huge amount of time (days)

Reference: Beerli P., Felsenstein J. 1999. Maximum likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152:763-773.

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MISAT

Web address: http://www.biom.cornell.edu/Homepages/Rasmus_Nielsen/files.html#MISAT

Description: estimates the likelihood surface for theta (4 times the effective population size times the mutation rate) for microsatellite data

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NewHybrids

Web address: http://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm#NewHybs

Description: implements a Gibbs sampler to estimate the posterior probability that genetically sampled individuals fall into each of a set of user-defined hybrid categories.

Reference: Anderson E.C., Thompson E.A. (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160: 1217--1229

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PAML

Web address: http://abacus.gene.ucl.ac.uk/software/paml.html

Description: PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
Possible uses of the programs are:

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PCAGEN

Web address: http://www.unil.ch/izea/softwares/pcagen.html

Description: Principal Components Analysis for genetic data

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PHYLIP

Web address: http://evolution.genetics.washington.edu/

Description: estimates phylogenies

Reference: Felsenstein J. 2001. PHYLIP 3.6. Department of Genetics, University of Washington.

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pop100gene

Web address: http://www.ensam.inra.fr/URLB/pop100gene/pop100gene.html

Description: computes allele frequencies, heterozygosity, etc.

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Relatedness

Web address: http://www.bioc.rice.edu/Keck2.0/labs/

Description: calculates average genetic relatedness among sets of individuals defined by demographic variables, either on average or by pairs

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RSTCalc

Web address: http://helios.bto.ed.ac.uk/evolgen/rst/rst.html

Description: estimates genetic differentiation measures from microsatellite data

Reference: Goodman, SJ 1997. Rst Calc: a collection of computer programs for calculating estimates of genetic differentiation from microsatellite data and a determining their significance. Molecular Ecology 6: 881-885.

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SAMOVA

Web address: http://web.unife.it/progetti/genetica/Isabelle/Isabelle.html

Description: This program implements a new approach to define groups of populations that are geographically homogeneous and maximally differentiated from each other. As a by-product, it also leads to the identification of genetic barriers between these groups. The method is based on a simulated annealing procedure that aims at maximizing the proportion of total genetic variance due to differences between groups of populations (SAMOVA, Spatial Analysis of MOlecular VAriance).

Reference: Dupanloup I., Schneider S., Excoffier L. 2002. A simulated annealing approach to define the genetic structure of populations. Molecular Ecology.

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STRUCTURE

Web address: http://pritch.bsd.uchicago.edu/

Description: The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including microsatellites, RFLPs and SNPs.

Reference: Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics. 2000 Jun;155(2):945-59.

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TCS

Web address: http://inbio.byu.edu/Faculty/kac/crandall_lab/programs.htm

Description: implements estimation of the TCS network (as described by Templeton et al. 1992, Genetics 132:619-633) from DNA sequences, or nucleotide distances. Also estimates other parameters, as the 95% parsimony limits and outgroup weights

References:
Clement M. Posada D. and Crandall K. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9(10): 1657-1660.
Templeton, A. R., Crandall, K. A. and Sing, C. F. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132:619-633.
For a review on networks and instraspecific genealogies: Posada D. and Crandall K.A. 2001. Trends in Ecology and Evolution 16 (1): 37-45