LAMARC (Likelihood Analysis with Metropolis Algorithm using Random Coalescence) is a program which estimates population-genetic parameters such as population size, population growth rate, recombination rate, and migration rates. It approximates a summation over all possible genealogies that could explain the observed sample, which may be sequence, SNP, microsatellite, or electrophoretic data.
PKreport aims to 1) provide automatic pipeline for users to visualize data and models. It creates a flexible R framework with automatically generated R scripts to save time and cost for later usage; 2) implement an archive-oriented management tool for users to store, retrieve and modify figures. 3) offer powerful and convenient service to generate high-quality graphs based on two R packages: lattice and ggplot2.
Partition is a model-based statistical software package for identifying population sub-division and assigning individuals to populations, on the basis of their genotypes at co-dominant marker loci. The underlying population genetic model is appropriate for out-crossing diploid organisms.
PartitionML is a program that searches for the best possible partition of a sample into independent panmictic clusters and simultaneously assign individuals to them using a maximum likelihood (ML) criterion.
PartitionView will read the partition output file, as it is being written, and will display the path of the Markov chain (see below) as it evolves in real time.
iAdmix is a program to estimate individual admixture proportions from DNA sequencing experiments (exome sequencing, targeted sequencing, low coverage whole-genome sequencing or genotyping)