ENT is a highly scalable genotype phasing algorithm based on entropy minimization. ENT is capable of phasing both unrelated and related genotypes coming from complex pedigrees.
::DEVELOPER
Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut
GEVALT (GEnotype Visualization and ALgorithmic Tool) is designed to simplify and expedite the process of genotype analysis and disease association tests by providing a common interface to several common tasks relating to such analyses. It is aimed for analysis of unrelated individuals as well as two-generation families.
RecMin is a software to identify ancestral recombination events from population genetic data.Under certain assumptions the pattern of diversity at a collection of linked sites provides information allowing us to detect historic recombination events. The program RecMin.c calculates a lower bound on the number of recombination events required to construct any history of a sample, under the assumption that each segregating site has mutated only once since the most recent common ancestor of the sample. Such a lower bound is appropriate, since many historical recombinations are typically undetectable. It gives a measure of what extent the sample history differs from a simple tree structure, and can show if there is regional clustering of the detectable recombinations.
ANCESTRYMAP finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. Admixture mapping is a method for localizing disease causing genetic variants that differ in frequency across populations. It is most advantageous to apply this approach to populations that have descended from a recent mix of two ancestral groups that have been geographically isolated for many tens of thousands of years: for example, African Americans have both West African and European American ancestry. The approach assumes that near a disease causing gene there will be enhanced ancestry from the population that has greater risk of getting the disease. Thus if one can calculate the ancestry along the genome for an admixed sample set, one could use that to identify disease causing gene variants. The figure below shows a schematic of how a disease locus would appear in an admixture scan of patients and controls.
adpaper is an R package. The package includes the source code for simulations and R scripts . This can be used to re-run simulations with different parameter values to explore how each influences the onset of fluctuations.
GRAMA (Genetic Recombinant Analysis and Mapping Assistant) is a new tool that automates TGCE data analysis for genetic mapping purpose. Data from multiple TGCE runs are integrated and displayed in an intuitive visual format. GRAMA includes its own algorithm to detect peaks in electropherograms, and peaks detected by GRAMA are automatically compared with those of another software package for any difference that will be flagged for user inspection. Analyses of the automatically combined genetic mapping results from GRAMA reveal high accuracy with virtually zero errors. Because of the accuracy of the calls and the intuitive interface, GRAMA boosts user productivity more than two-fold relative to previous manual methods.
GRAMA: genetic mapping analysis of temperature gradient capillary electrophoresis data. Philip M. Maher, Hui-Hsien Chou, Elizabeth Hahn, Tsui-Jung Wen and Patrick S. Schnable. Theoretical and Applied Genetics Online First, April 2006. DOI: 10.1007/s00122-006-0282-6
SCAT (Smoothed and Continuous AssignmenTs) implements a Bayesian statistical method for estimating allele frequencies and assigning samples of unknown (or known) origin across a continuous range of locations, based on genotypes collected at distinct sampling locations. In brief, the idea is to assume that allele frequencies vary smoothly in the study region, so allele frequencies are estimated at any given location using observed genotypes at near-by sampling locations, with data at the nearest sampling locations being given greatest weight.