The
Tree of Life (Phylogeny)
PHYLIP:
Phylogeny Inference Package (J.
Felsenstein)
PhylPro
Phylogenetic Profile methods for detecting genetic
recombination.
POPGENE: Software for Population Genetics Analysis
Program designed for the analysis of co-dominant and
dominant markers using haploid and diploid data. POPGENE
computes both comprehensive genetic statistics (e.g.,
allele frequency, gene diversity, genetic distance, G-statistics,
F-statistics) and complex genetic statistics (e.g., gene
flow, neutrality tests, linkage disequilibria, multi-locus
structure).
Relatedness
Calculates average genetic relatedness among sets of
individuals defined by demographic variables, either on
average or by pairs. It finds standard errors and
confidence intervals for signifiance testing using a
jackknife resampling method.
Goodnigth
software: Recopilation of other software for population
biology
RAPDistance
(John Armstrong, Adrian Gibbs, Rod Peakall, Georg Weiller)
SiScan
"Sister-scanning" to identify recombination in
sequence data.
TFPGA -
Tools for Population Genetic Analyses
Windows program for the analysis of allozyme and molecular
population genetic data. This program calculates
descriptive statistics, genetic distances, and F-statistics.
It also performs tests for Hardy-Weinberg equilibrium,
exact tests for genetic differentiation, Mantel tests, and
UPGMA cluster analyses.
Spectrum
A Mac program designed to read in a data file comprising
aligned character
arrays (such as DNA sequence data) or distance data in the
form of a matrix, and perform somesimple spectral analysis
procedures on that data.
Structure
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.
TreeMap
Experimental program for comparing host and parasite
phylogenies. Reads PHYLIP and PAUP tree files, and data
COMPONENT files. Program comes with example data files and
documentation in Postscript. The versions for the Mac and
for Windows are essentially identical.
TreeView:
Tree drawing software
VOSTORG
A package of microcomputer programs for sequence analysis
and construction of phylogenetic trees.
WinAMOVA
v 1.55
A graphical Windows 3.x program for the analysis of
population genetic structure from molecular or
conventional genetic data. This program is also embedded
into Arlequin.
