COANCESTRY is a computer program that implements 7 methods to estimate the pairwise relatedness between individuals and 4 methods to estimate individual inbreeding coefficients, using individual genotypes at a set of marker loci.
Stacks is a software pipeline for building loci out of a set of short-read sequenced samples. Stacks was developed for the purpose of building genetic maps from RAD-Tag Illumina sequence data, but can also be readily applied to population studies, and phylogeography.
BiNoM (Biological Network Manager )is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX) and to carry out studies on the network structure. BiNoM provides the user with a complete interface for the analysis of biological networks in Cytoscape environment.
The SLiMSuite collection contains a number of open-source bioinformatics tools to analyse these important protein features. The main programs in SLiMSuite are: SLiMFinder, SLiMSearch, QSLiMFinder, SLiMDisc, SLiMPred, SLiMPrints, CompariMotif, SLiMMaker, PRESTO and GOPHER.
AgileKnownSNPFilter analyses sequence variants exported by AgileAnnotator and identifies those that have previously been found by the 1000 Genomes Project.
ChIPMonk is a program designed to help in the visualisation and analysis of ChIP-on-chip array data. It provides a comprehensive set of tools to import, normalise, analyse and visualise your data.
popoolation 1.2.2 / PoPoolation2 1.201 / PoPoolation TE 1.02
:: DESCRIPTION
PoPoolation is a collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals
PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences.
PoPoolation TE is a quick and simple pipeline for the analysis of transposable element insertions in (natural) populations using next generation sequencing.
PhyloGenie is a PERL script combining the various steps necessary to producing a phylome. BLAST or PSIBLAST searches are performed for all FASTA format sequences in an input file, the HSP’s corresponding to user defined selection criteria (E-value, coverage, score per column, identity) are extracted and used as a basis for multiple sequence alignment. Phylogenies can then be infered using the supplied standard NJ method or any other program accepting aligned FASTA sequences as input and generating Newick format trees. As analysis of phylogenies is far more complex than analysis of BLAST results we also provide a tool to filter a set of phylogenetic trees for those corresponding to user defined topological selection criteria.
