Search Results for "genetics"

Nemo is an individual-based, forward-time, genetically explicit, and stochastic simulation software designed for the study of the evolution of life history and quantitative traits, and genetic markers under various types of selection, in a spatially explicit, metapopulation framework.

The MIQAS project (Minimal Information for QTL and Association Studies) provides a standard for reporting of QTL and association studies in genetics (similar to the MIAME standard for microarray data).

Mendel’s Accountant is a biologically realistic, forward-time, parallel, numerical simulation program which models genetic change within a population, as affected by mutation and selection.

Main application is twofold: first to convert genotype SNP data into formats of different imputation tools like PLINK MACH, IMPUTE, BEAGLE and BIMBBAM, second to transform imputed data into different file formats like PLINK, HAPLOVIEW, EIGENSOFT and SNPTEST. Readable file formats: plink-pedigree (ped and map), plink-raw, plink-dosage, mach , minimac, impute, snptest, beagle and bimbam. Similarly all kinds of imputation of outputs are also accepted. Formats which can be generated by...

Application to estimate haplotypes and other genetics data, based on maximum likehood approach. It can handle present-absent as well as multiallelic loci.

A general-purpose individual-based forward-time population genetics simulation environment

SysGenSIM is a bioinformatics toolbox to create artificial gene expression datasets by simulating Systems Genetics experiments.

This project assists you in performing population genetic analyses by taking over the ugly, boring and error-prone data manipulation steps. Starting from well specified input formats VCF, BED and FASTA and a unique configuration file describing data (f.e. from SNP-arrays or sequencing) as well as filtering one can create standard POPGEN formats like Eigenstrat, PEDMAP (PLINK), Treemix ... In addition there are several utilities for * generating VCF from SNPArray data (NCBI - GEO,...

Development of exact and approximate methods (Importance Sampling and MCMC based) for computing likelihoods under the standard population genetic models of mutation,migration & recombination. Project issues are mainatined at https://freecode4susant.atlassian.net/browse/COALESCENT

POPBAM is a tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome.

parastructure is a perl script collection to run the population genetics software STRUCTURE from Pritchard et al. 2000 (http://pritch.bsd.uchicago.edu/structure.html) in parallel on a cluster (beowulf type). Each run of K (the number of populations) is executed separately on each CPU of the cluster trough queue system based on PBS. A summary statistics table and distruct figures (Noah Rosenberg: http://www.stanford.edu/group/rosenberglab/distruct.html) are built at the end of the run. ...

Java forward population genetics simulation tool similar to 'ms'

Assimilator is a molecular genetics tool to inform selection of associated genetic variants for functional studies

Opensource software projects for genetics and genomics from Sage Bionetworks.

A small simulator for Mendelian genetics, genetic drift, natural selection and random mutations, built on matplotlib and wxpython. A graph will be generated that traces the distribution of genotypes at successive generations.

The goal of the GeneText project is the development of a software package that will enable users to dynamically generate an information summary page from multiple sources given a search term. Fields of interest are biology, genetics and bioinformatics.

Biological sample supervisor. Plant material and more (cellular, genetics).

a cross-platform framework and environment for haplotype analysis with a special focus on human and medical genetics in python/wxpython

GeXpert is an expert system that can be used for genetics and metabolic pathway analysis. GeXpert can help Biotechnologists do their work faster, reducing the time required for performing, analyzing and storing the results of Bioinformatics research.

GENtle is a free multipurpose tool for genetics and biochemistry. It manages DNA and amino acid sequences, does PCR, restriction, ligation, sequence annotation etc.

The Cybertory™ Virtual Molecular Biology Laboratory is an on-line virtual environment for conducting simulated experiments in molecular genetics.