Institute of Evolutionary Biology - Software for genetic analysis

RSTCALC, a DOS-based program for performing analyses of population structure, genetic differentiation and gene flow using microsatellite data. RSTCALC calculates unbiased estimates of RST and assesses their significance using bootstrap and permutation tests. RSTCALC was written by Simon Goodman.

CERVUS, a Windows package for parentage analysis using a likelihood approach. Taking co-dominant marker data in text format, CERVUS calculates allele frequencies, runs simulations and carries out parentage analysis within a single, easy-to-use framework. CERVUS was written by Tristan Marshall.

ANALYSE, a MacOS/PowerPC application for the analysis of hybrid zone data. Analyse was written by N. H. Barton and Stuart Baird.

PROSEQ, Processor of Sequences (ProSeq) is a Windows 95 / NT program for convenient sequence alignment editing and various population-genetic analyses. PROSEQ was written by Dmitry Filatov.

SWEEP BOTT, a program in ANSI C dedicated to the detection of bottlenecks and selective-sweeps from a coalescence-based maximum-likelihood analysis of DNA sequence polymorphism data. SWEEP BOTT must be compiled before it can be run. This program was written by Nicolas Galtier, University of Montpellier.

MULTILOCUS PACKAGE, a (platform independent) Mathematica package for studying multilocus population genetic models. The Multilocus Package is written by Nick Barton.

Link to MIXEDFAMILIES, a Mathematica package for detecting the presence of subfamilies in batches of offspring using genetic markers.
This program was written by Tim Vines: please see his website for details.

POOLMAP implements an algorithm for linkage disequilibrium mapping (a.k.a. association mapping) in a case-control design, which can be applied when the data are collected using DNA pools. Binaries and C code written by Toby Johnson.

Research-related material

Introgression through rare hybridisation: a genetic study of a hybrid zone between red and sika deer (genus Cervus) in Argyll Scotland. Appendix, data and analysis methods from this study. Supplied as downloadable Mathematica 3.0 note books.

PartiGene. The Blaxter Neglected Genomics lab software solutions for processing and analysis of expressed sequence tags are available from the PartiGene web-site.