Software Programs for Analysing Genetic Diversity

Arlequin

Schneider, S., D. Roessli and L. Excoffier. 2000. Arlequin: A Software for Population Genetics Data Analysis, Version 2.000. Genetics and Biometry Laboratory, Dept. of Anthropology, University of Geneva, Switzerland.

CLUSTAL W  

Thompson, J.D., D.G. Higgins and T.J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.

DnaSP

Rozas, J. and R. Rozas. 1995. DnaSP, DNA sequence polymorphism: an interactive program for  stimating population genetics parameters from DNA sequence data. Comput. Appl. Biosci. 11:621-625. 

GDA

Lewis, P.O. and D. Zaykin. 1999. Genetic Data Analysis: Computer Program for the Analysis of Allelic Data, Version 1.0 (d12). Distributed by the authors.

GENEPOP

Raymond, M. and F. Rousset. 1995. GENEPOP (version 1.2): Population genetics software for exact tests and ecumenicism. J. Hered. 86:248-249.

GeneStrut

Constantine, C.C., R.P. Hobbs and A.J. Lymbery. 1994. FORTRAN programs for analysing population structure from multilocus genotype data. J. Hered. 85:336-337.

MacClade

Maddison, D.R. and W.P. Maddison. 2000. MacClade. Version 4. Sinauer Associates, Sunderland, MA.

MALIGN

Janies, D. and W.C. Wheeler. 1998. MALIGN.pdf: Documentation for MALIGN, software for multiple alignments of DNA sequences. Distributed by the

MEGA2

Kumar, S., K. Tamura, I.B. Jakobsen and M. Nei. 2001. MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17(12):1244-1245.

NTSYSpc

Rohlf, F.J. 2002. NTSYS pc: Numerical Taxonomy System, Version 2.1. Exeter Publishing, Setauket, NY.

PAUP*

Swofford, D.L. 2002. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4. Sinauer Associates, Sunderland, MA.

PHYLIP

Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package), Version 3.5c. Distributed by the author.

POPGENE

Yeh, F.C., R.C. Yang, T.B.J. Boyle, Z.H. Ye and J.X. Mao. 1997. POPGENE, the User-Friendly Shareware for Population Genetic Analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Canada.

PowerMarker

Liu, J. 2003. PowerMarker: New Genetic Data Analysis Software, Version 3.0. Free program distributed by author over Internet at <http://www.powermarker.net>

SITES

Hey, J and J. Wakeley. 1997. A coalescent estimator of the population recombination rate. Genetics 145:833-846.

Structure

Pritchard, J.K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.

TFPGA

Miller, M.P. 1997. Tools for Population Genetic Analysis (TFPGA), 1.3: A Windows Program for the Analysis of Allozyme and Molecular Population Genetic Data. Distributed by the author.

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