Allele

Using Affymetrix CEL files as its source, this script combines quantile normalized SNP A and B probe intensities for each marker into a theta value, then calculates B-Allele Frequencies for each marker. For information on accessing B Allele Frequencies for Illumina data, Platforms: Mac

This program, BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model. One of the simplest possible scenarios covered consists of an island model in... Platforms: Windows, Mac, Linux

This script scans for allele names (e.g. 1,2,3,4) and prompts for new names (e.g. A,C,G,T). Missing alleles remain missing. Platforms: Mac

Bio::PopGen::IO contains input individual,marker,allele information. SYNOPSIS use Bio::PopGen::IO; my $io = new Bio::PopGen::IO(-format => csv, -file => data.csv); # Some IO might support reading in a population at a time my @population; while( my $ind = $io->next_individual ) { push... Platforms: *nix

This script converts categorical genotypes such as AA, AG without a delimiter to the standard genotype format accepted by Golden Helix SVS (A_A, A_G, etc). The script prompts for the missing value indicator. Possible uses include converting genotype columns after importing data that were... Platforms: Mac

A program for estimating 2Ns from temporal allele frequency data. Part of the research focus of my group is the developent of phylogenetic and statistical genetic approaches. A number of these have been further developed into scientific software. The software below can be either downloaded... Platforms: Mac

This script recodes AGCT alleles to the standard genotype format of A_A, A_B, and B_B. Prompts for a marker map strand field to use for recoding. The strand field must have allele information in the form [C/T]. Missing genotypes remain missing. Platforms: Mac

This script imports multiple fields of data from Illumina Final Report text files. It can be used to just import genotype data, or multiple real-valued columns such as B-Allele Frequency, or Log R Ratios. The user can choose from all fields found in the text file and select which ones should be... Platforms: Mac

PGAPy is a wrapper for pgapack, the parallel genetic algorithm library, a powerfull genetic algorithm library by D. Levine, Mathematics and Computer Science Division Argonne National Laboratory. The library is written in C. PGAPy wraps this library for use with Python. The original pgapack... Platforms: *nix

PGDSpider was built using the Java programming language as a conversion app for population genetics and genomics programs. The software facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic... Platforms: Windows

The advent of massively parallel sequencing technologies has fundamentally changed the study of genetics. New platforms like the Illumina GAIIx and the Roche GS yield unprecedented levels of sequencing throughput. The analysis and interpretation of data from next-generation sequencing platforms... Platforms: Windows

Olorin is an interactive filtering utility built using the Java programming language. The program can be used for next generation sequencing data coming from the study of large complex disease pedigrees. Olorin, is a tool which integrates gene flow output from Merlin and next generation... Platforms: Windows

bint was written for the purpose of obtaining subsets of intensity data from genotyping assays. Either the X & Y intensities for creating cluster plots or Log R Ratio and B Allele Frequencies for CNV detection. Extracting the data for individual SNP/CNV markers or individual samples was slow... Platforms: Windows, Mac, BSD, Linux

The C++ library for bioinformatics and artificial intelligence. Basic abstractions (like attribute, domain, state, etc.), DNA primitives (Nucleotide, Chain, EnergyNucleo, SecStruct, FoldedChain, FoldedPair, Codon, CodonAminoTable, Nussinov algorithm), population genetics primitives (Allele,... Platforms: Mac

GenoDive is a Mac-only program for population genetics analyses. The present version is a beta, which means that it will still contain bugs, and some analyses are not yet fully implemented. Please report any issues, bugs or praise that you may have to the author. This version should work on Mac... Platforms: Mac

This script imports Affymetrix DMET data. Hemizygous markers are converted to homozygous markers, and tri-allelic markers are converted into two columns, each containing the major allele and one of the minor alleles. A DMET marker map (see below) can be selected after selecting the DMET report... Platforms: Mac

Olorin is an interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. Olorin, is a tool which integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based... Platforms: Mac