PCR Analyzer is a software to estimate the initial amount of amplicon using a simplified mechanistic model based on chemical reactions in the annealing step of the PCR.
EH is a program to test and estimate linkage disequilibrium between different markers or between a disease locus and markers. This is an updated version in which the previous “disease” (case-control) option has been deleted (but see below how to work with case-control data).
LAPD (Linkage Analysis Using Pedigree Data) allows to estimate maximum likelihood allele and two-locus haplotype frequencies, using an Expectation-Maximization algorithm, taking into account family relationships of the individuals.
Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. Migrate uses maximum likelihood or Bayesian inference to jointly estimate all parameters.
It can use the following data types:
Sequence data using Felsenstein’s 84 model with or without site rate variation,
Single nucleotide polymorphism data (sequence-like data input, HAPMAP-like data input)
Microsatellite data using a stepwise mutation model or a brownian motion mutation model (using the repeatlength input format or the fragment-length input format),
Electrophoretic data using an ‘infinite’ allele model.
Genie (Genealogy Interval Explorer) is a program for the inference of demographic history from reconstructed molecular phylogenies. It is primarily designed for the analysis of phylogenies reconstructed from highly variable viral gene sequences, but can be applied to other types of sequence data that contains a significant amount of phylogenetic information.
SLIM (Sliding Linear Model) is a software to more reliably estimate π(0) under dependence. When tested on a number of simulation datasets with varying data dependence structures and on microarray data, SLIM was found to be robust in estimating π(0) against dependence. The accuracy of its π(0) estimation suggests that SLIM can be used as a stand-alone tool for prediction of significant tests.