Genotype

LDMgen is a small, easy to use, command prompt based application specially designed to offer users a tool to help you map the disease gene (including location and confidence interval) by using multisite genotype data of case-control studies. The application comes with a default parameters file.... Platforms: Windows

CoNIFER, also knows as Copy Number Inference From Exome Reads is a Python-based tool that uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. As exome capture reactions are subject to strong and systematic capture biases between sample... Platforms: Windows

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

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

UNPHASED is a small, simple, Java based application specially designed to offer users a versatile tool for performing genetic association analysis. This utility implements maximum-likelihood inference on haplotype and genotype effects while allowing for uncertain phase and missing genotypes.... Platforms: Windows

Inference of recent migration rates between populations using multi-locus marker genotype data. Platforms: Windows, Mac

sibsim is designed to simulate either genotype and/or quantitative phenotype data in family structures in a modern, easy to use and highly scaleable way. sibsim is based on XML, completely written in C++ and published under the GNU General Public License Platforms: Mac, BSD, Solaris, Linux

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

sibsim is designed to simulate either genotype and/or quantitative phenotype data in family structures in a modern, easy to use and highly scaleable way. sibsim is based on XML, completely written in C++ and published under the GNU General Public License Platforms: *nix

MB Blood Type Inheritance is a blood type determination tool for your child. This is based on the genetic inheritance of a blood type from a parent to a child. Blood Type describes the composition of a personls red blood cells. It is determined by co-dominant alleles. This is one of the forms in... Platforms: Windows

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Jenetics is a Java based object oriented library of an Genetic Algorithm. The library offers a clear separation of the several concepts of the algorithm, e.g. Gene, Chromosome, Genotype, Phenotype, Population and FitnessFunction. for WindowsAll Platforms: Windows

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Pedimap is a tool for exploring and visualizing the flow of phenotypes and alleles (observed or based on Identity-by-Descent calculations) through pedigrees. It has tools for the manual and automatic selection of parts of the pedigree based on criteria such as ancestors and/or progeny to a... Platforms: Windows

An object oriented library of an Genetic Algorithm, implemented in Java. Clear separation of the several concepts of the algorithm, e.g. Gene, Chromosome, Genotype, Phenotype, Population and Fitness Function. The fitness calculation is parallelized. Platforms: Windows, Mac, Linux

TASSEL is a bioinformatics software package that can analyze diversity for sequences, SNPs, or SSRs. Genotype/phenotype associations can be carried out by GLM or a mixed model. Estimates distance and linkage disequilibrium statistics. Platforms: Windows, Mac, Linux

This script takes genotypes from two different arrays and creates a consensus spreadsheet, and two optional spreadsheets. In order to run this script two spreadsheets of mapped genotype data are required. The spreadsheets may also contain non-marker mapped columns as they will be skipped when... Platforms: Mac