Beebee & Rowe: An Introduction to Molecular Ecology: 2e 
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Chapter 05
Useful Software
GENEPOP(Raymond and Rousset 1995)
Available to download or to use on the web, estimates compliance with Hardy–Weinberg equilibrium, linkage equilibrium, allele frequencies, F and R-statistics and isolation by distance.
http://genepop.curtin.edu.au/
FSTAT (Goudet 1995)
Estimates observed and expected heterozygosities, allelic richness, F and R-statistics.
http://www2.unil.ch/popgen/softwares/fstat.htm
ARLEQUIN (Schneider et al. 2000)
Estimates genetic diversity, genetic distances, population structure using analysis of molecular variance (AMOVA), with a wide range of molecular data including DNA sequences, codominant and dominant markers.
http://anthro.unige.ch/arlequin/
NeESTIMATOR (Peel et al. 2004)
Uses a range of different methods to estimate effective population size from molecular marker data.
www.dpi.qld.gov.au/cps/rde/dpi/hs.xsl/28_6908_ENA_HTML
BOTTLENECK (Cornuet and Luikart 1996)
Uses molecular marker data to estimate the likelihood of recent population bottlenecks.
http://www.montpellier.inra.fr/URLB/bottleneck/bottleneck.html
STRUCTURE (Pritchard et al. 2000)
Uses molecular marker data to estimate numbers of genetically distinct populations in a sample, and the extent of admixture between them.
http://pritch.bsd.uchicago.edu/software.html
BAPS (Corander et al. 2003)
Uses molecular marker data to estimate population structure, especially numbers of distinct clusters (populations or subpopulations). Includes possible use of a spatial model.
http://www.abo.fi/fak/mnf/mate/jc/smack_software_eng.html
BAYESASS (Wilson and Rannala 2003)
Uses genotype data to estimate numbers of recent migrants in populations.
http://sites.google.com/site/rannalaorg/software
IM (Hey and Nielsen 2004)
Estimates population sizes, migration rates and divergence times of population pairs.
http://lifesci.rutgers.edu/~heylab/HeylabSoftware.htm#IM
GENELAND (Guillot et al. 2005)
Uses geographical and genetic data to infer population structure and the physical locations of genetic discontinuities.
http://www2.imm.dtu.dk/~gigu/Geneland/
Useful Websites
Completed genomes
www.ebi.ac.uk/genomes
Microarray database
www.ebi.ac.uk/arrayexpress
Molecular interactions, relevant to systems biology studies
www.ebi.ac.uk/intact
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