Genetics softwares

January Weiner 3rd. Ped-sim enables simulations of data for individuals from a given pedigree structure. It can use sex-specific genetic maps to incorporate differences in male and female recombination events. Williams lab. Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives. PLoS Genet. Hapi is a program that efficiently infers minimum recombinant and maximum likelihood haplotypes for nuclear families.

Genome Biol. Epub Oct Rapid haplotype inference for nuclear families. In a second phase, the molecular genetic diversity of one or several samples drawn from the simulated species can be generated. Bioinformatics, Volume 26, Issue 3, Page Mol Biol Evol. Epub Jan 9. RUNTC is an estimator of first coalescent time, which is the time when a copy of a gene most recently shared ancestry with other copies of that gene.

This is also an estimate of the upper bound of when a mutation has arisen, and it can be used to study the ages of alleles that are found in a population. An estimator of first coalescent time reveals selection on young variants and large heterogeneity in rare allele ages among human populations.

HKA is a computer program that carries out the widely used statistical test for natural selection. The focus of the software is to infer tree models that relate genetic aberrations to tumor progression. Many improvements in version 3. The radiation hybrid mapping methods are based on: a new strategy to select framework markers, a known reduction from the radiation hybrid mapping problem to the traveling salesman problem, and using the existing software CONCORDE to solve large instances of the traveling salesman problem.

The map construction software was used at NCBI to construct dense human radiation hybrid maps. Follow the link on the right to learn more about these maps. The software has also been used to construct maps of the cat and the dog, which are described in some of the references, as well as other vertebrates.

Christophe Hitte University of Rennes, France constructed the maps of the dog and independently compared our software to other, competing packages.