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Arlequin 3.5

Offers a large set of methods and statistical tests for population genetic analysis of marker and sequence data, including AMOVA (see also GenAlEx). Nice graphical user interface but peculiar input format for marker data can frustrating (GenAlEx is nicer in this regard). Java based, available for Mac, Windows, and Unix operating systems.

CERVUS

CERVUS is a Windows 95-based program designed for large-scale parentage analysis using co-dominant loci. Analysis is broken down into three sequential stages. Using genotype data in text file format, the program can analyse allele frequencies, run appropriate simulations and carry out likelihood-based parentage analysis, testing the confidence of each parentage using the results of the simulation. Simulations may also be used to estimate the power of a series of loci for parentage analysis, using real or imaginary allele frequencies.

FSTAT

FSTAT is a computer package for PCs which estimates and tests gene diversities and differentiation statistics from codominant genetic markers. It computes both Nei and Weir & Cockerham families of estimators of gene diversities and F-statistics, and tests them using randomization methods (see also GDA and TFPGA).

Genetic Data Analysis Software

The primary feature of GDA, short for Genetic Data Analysis, is that it implements the analysis of variance based estimators of Wright's F-statistics advocated by Weir and Cockerham (1984) and Weir (1996) and uses randomization procedures to construct confidence limits about the estimates (see also Fstat and TFPGA). In addition, it calculates basic descriptive statistics, and implements test of linkage disequilibrium. Nice user interface but peculiar input data formatting. Available for Windows.

GenAlEx

GenAlEx, short for Genetic Analysis in Excel, is a user-friendly cross-platform package for population genetic analysis. Functions include AMOVA (see also Arlequin), spatial autocorrelation (see also SPAGeDI), Mantel tests (see also Permute! and TFPGA), and principle component analysis of genetic data. It runs within Microsoft Excel and so is not operating system specific. GenAlEx enables population genetic data analysis of codominant, haploid and binary genetic data providing analysis tools applicable to plants and animals.

GeneClass 1 & 2

GeneClass2, short for Genetic Classification, is a program employing multilocus genotypes to select or exclude populations as origins of individuals. Functions include the assignment of individuals to populations and detection of migrants (see also Structure and WhichRun). This command-line program is available for Linux and Windows.

GENEPOP

Web server based software that estimates a variety of population genetic parameters and conducts a variety of sophisticated tests for departures from Hardy-Weinberg, population differentiation, and linkage disequilibrium. It also can convert data files to formats for use with other programs, including Arlequin. Because Genepop runs on the web, it is not operating system specific. If your interest is Wright'sF-statistics, Fstat, GDA, and TFPGA are recommended.

Isolation by Distance Web Service

IBDWS, short for Isolation by Distance Web Service, is a web server based application for analyzing the relationship between (genetic) isolation and (geographic) distance. IBDWS works with both diploid genetic marker and haploid DNA sequence data, and for genetic distances calculates Wright's Fst (or PhiST for sequence data), Slatkin's M-hat, and Roussett's linearized Fst. Be sure to the the About IBDWS page for helpful information about using the program: http://ibdws.sdsu.edu/~ibdws/aboutibdws.html

Permute!

Not population genetics software per se but very handy for conducting multiple regression over distance with permutation tests (e.g, Mantel test; see also GenAlEx and TFPGA). Unlike other programs can conduct permuation tests using non-square matrices (important in some contexts). Nice user interface with simple input format. Available for the Mac only (a Classic application).

PHYLIP

A modular set of programs for phylogenetic analysis. Primarily aimed at the analysis of sequence data, but modules also available for genetic distance estimation, the construction of neighbor-joining and UPGMA trees, and bootstrapping with respect to marker data. Command line interface and peculiar input data format. Available for a variety of operating systems.

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