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Beebee & Rowe: An Introduction to Molecular Ecology: 2e

Chapter 07

Useful Software

ARLEQUIN (Schneider et al. 2000)
Estimates genetic diversity, genetic distances, population structure using analysis of molecular variance (AMOVA), and mismatch distribution analysis with a wide range of molecular data including DNA sequences, codominant and dominant markers.
http://anthro.unige.ch/arlequin/

GEODIS 2.5 (Posada et al. 2000)
Implements nested clade analysis when given a nested cladogram, which can be generated after using the program TCS.
http://darwin.uvigo.es/software/geodis.html

IM (Hey and Nielsen 2004)
Estimates population sizes, migration rates and divergence times of population pairs.
http://lifesci.rutgers.edu/~heylab/HeylabSoftware.htm#IM

MRBAYES 3.1 (Huelsenbeck and Ronquist 2001)
Bayesian method for tree construction assuming prior distributions of tree topologies and inferring posterior distributions of topologies.
http://mrbayes.csit.fsu.edu/

PAUP* (Swofford 1996)
A widely used, but not free, phylogeny package incorporating many different methods including MODELTEST for determining the most appropriate model of evolution for individual data sets.
Details are available at http://www.sinauer.com The international distributor is W. H. Freeman at Macmillan Press, Brunel Road, Houndsmills, Basingstoke, Hampshire RG21 6XS, U.K.

PHYLIP 3.66 (Felsenstein 1993)
A package of many different programs for generating phylogenetic trees.
http://evolution.genetics.washington.edu/phylip.html

TCS 1.21 (Clement et al. 2000)
Estimates gene genealogies and generates haplotype networks, e.g. from mtDNA haplotype sequence data.
http://darwin.uvigo.es/software/tcs.html