:: DESCRIPTION
PEDIG is a fortran software suited to the analysis of very large populations (up to several tens of million individuals).
::DEVELOPER
D. Boichard (contact author), INRA
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
GERMLINE is a program for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe’er I (2008)
Whole population, genomewide mapping of hidden relatedness.
Genome Research.2009 Feb;19(2):318-26.
:: DESCRIPTION
FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations. Unlike coalescent-based simulation tools, such as MS (Hudson, 2002), FREGENE works forwards-in-time which allows a wide range of demographic and selection scenarios to be implemented. Many such models are already incorporated into FREGENE, and since it is open source users can modify or extend these. Coalescent methods have difficulty incorporating large amounts of gene conversion or crossover (Hoggart et al. 2007), whereas these pose no particular problem for FREGENE. FREGENE offers a flexible model for recombination hotspots, and can readily simulate regions up to tens of Mb on a standard desktop computer.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Balding DJ (2008).
FREGENE: Simulation of realistic sequence-level data in populations and ascertained samples .
BMC Bioinformatics 2008, 9:364
