SPIP (simulate pedigrees in populations) simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user. Numerous variables controlling the age structure of the population, the number of offspring produced, the variance in male and female reproductive success, survival rates of different age classes, mate fidelity, duration of simulation, etc. can be specified by the user.
PhyloMapper can be used to estimate phylogeographic history using genetic data. The statistical model implemented in PhyloMapper is unique in that it can be used as a descriptive tool and/or to test a priori hypotheses
The GDL (Genetic Data analysis Library) is a dynamic C library that aims at providing low level and high level Application Programming Interface (API) to manage and analysis various genetic and genomic data types.
PATRI (PaTeRnity Inference) is a program for paternity analysis of genetic data. The program requires genotypic, diploid data from one or more loci from mother-offspring pairs and from potential fathers. Typical data might include microsatellite markers, Restriction Fragment Length Polymorphisms (RFLPs) or Single Nucleotide Polymorphisms (SNPs). Given such genotypic data, PATRI can calculate posterior probabilities of paternity for all sampled offspring. When behavioral or ecological information can be used to divide the sampled males into different groups, PATRI can perform maximum likelihood analyses of hypotheses regarding the relative reproductive success of those groups.
Structurama is a program for inferring population structure from genetic data. The program assumes that the sampled loci are in linkage equilibrium and that the allele frequencies for each population are drawn from a Dirichlet probability distribution. The method implements two different models for population structure. First, Structurama implements the method of Pritchard et al. (2000) in which the number of populations is considered fixed. The program also allows the number of populations to be a random variable following a Dirichlet process prior (Pella and Masuda, 2006; Huelsenbeck and Andolfatto, 2007).
PhyNav (Phylogenetic Navigator)is a tree sampling method to reconstruct phylogenetic trees from really large datasets (DNA and protein). The method combines different methods to sample good trees.
Hickory provided here implements the Bayesian method described in Holsinger (1999) for estimating F-statistics co-dominant marker data and the method described in Holsinger et al. (2002) for estimating F-statistics from dominant marker data. It also includes routines to allow posterior comparisons as described in Holsinger and Wallace (2004).
GenoPlayer is a software which is useful for visualization and manual refinement of MapPop results. Genome analysis based on molecular markers can generate large amount of information. A graphical display and visualization of the data provides a powerful overview of information and can simplify interpretation. We developed a JAVA software package, GenoPlayer, for visualizing and querying genetic linkage data. The program displays chromosomal genotypes of individuals based on molecular marker data. GenoPlayer can be used to select informative markers, to identify the most useful individuals in a segregating population, to detect segregation distortion, and to detect errors in the data.