PDA: Pipeline Diversity Analysis
PDA is a Web Server that automatically can search for polymorphic sequences in large databases and estimate their genetic diversity in different functional regions. The output includes a database with the sequences and estimations, the performed alignments and a histogram maker tool.
PopDrowser. Navegador para la representación de la diversidad genómica de 158 genomas de Drosophila melanogaster. Incluye las secuencias de DNA, las anotaciones genómicas, las estimas de diversidad nucleotídica, y calcula diversos test estadísticos para determinar el efecto de la selección natural a nivel nucleotídico.
Automatic Alignments
Arlequin (v2000); Population Genetics Software
An exploratory population genetics software environment able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites), while retaining the capacity of analyzing conventional genetic data (standard multi-locus data or mere allele frequency data).
BOTTLENECK
Program for detecting recent effective population size reductions from allele data frequencies.
CAIC: Comparative Analysis by Independent Contrasts
ClustalW
DnaSP; DNA Sequence Polymorphism
DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguadé (1987), Tajima (1989), McDonald and Kreitman (1991), and Fu and Li (1993) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent.
Kinship
A program to perform maximum likelihood tests of pedigree relationships between pairs of individuals in a population.
LAMARC - Likelihood Analysis with Metropolis Algorithm using Random Coalescence
Package of programs for computing likelihoods for samples of data (DNA sequences and electrophoretic polymorphisms) from populations. Programs use coalescence theory, and estimate population parameters like effective population size, growth rate, and migration rate.
MacClade
A friendly Macintosh program primarily for analysis of categorical or state characters. Includes spreadsheets and graphical manipulation of trees.
MEGA
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).
Population Genetics in R
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.
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.
