LDWP (Linked Region Detection without Pedigree) is a software package for linkage analysis that finds the mutation regions for the case where the input individuals are closely related, but the pedigree is not known. A typical example is that in the pedigree below the individuals in the dotted rectangle are closely related,and the genotype data of them are known, whereas the genotype data of individuals outside the dotted rectangle are not available and even the pedigree may not be clear. LDWP takes the genotype data of the individuals in the dotted rectangle and the diagnoses (diseased or normal) information of each individual in the dotted rectangle as its input, and report the mutation regions.
LIden determines allele sharing status among family members using high-density SNP data. It takes SNP genotype data, pedigree structure and physical-locus-file as input, and outputs allele sharing graphical display files and linked regions
HAPAR (Haplotype Inference by Parsimony) is a program to infer haplotype from genotype data. It uses the parsimony principle, i.e. try to find the minimum number of haplotypes that can reconstruct the input genotypes.
LUCA (Likelihood Under Covariate Assumptions) is an R package implementing the methods for case-control inference of statistical interaction between genetic and nongenetic risk factors under covariate assumptions.
PGEToolbox is a Matlab-based software package for analysis of polymorphism and divergence data for population genetics and evolution. It estimates several basic statistics of DNA sequence variation and carries out statistical tests of selective neutrality under the infinite alleles model, such as Tajima’s D test, Fu & Li’s tests and Fay & Wu’s H test. The significance of tests is determined from the distribution of the statistics obtained by coalescent simulation. The toolbox performs McDonald-Kreitman test (and several extensions). PGEToolbox also contains functions for handling SNP (Single Nucleotide Polymorphism) genotype data. PGEToolbox is open-sourced, can be easily extended or tailored for specific tasks, and scaled up for large data sets.
MBEToolbox is a tool which aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned Matlab users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution.
BPrimm (Bayesian and Penalized regression in multiple loci mapping) includes a set of tools for simultaneously multiple loci mapping, and two novel methods named the Bayesian adaptive Lasso and the Iterative Adaptive Lasso
Pool-hmm aims at estimating allele frequencies and detecting selective sweeps, using NGS data from a sample of pooled individuals from the same population.