MIXMUL (Mixture of Weighted Multinomial) procedure is a convenient haplotype inference tool for mixed data to estimate haplotype frequencies accurately and output the most likely reconstructed haplotype pairs of each subject in the estimation.
MutaGeneSys (Mutation Genome System) uses genome-wide genotype data to estimate individual disease susceptibility. Our system integrates three data sources: the International HapMap project(hapmap.org), whole-genome marker correlation data (description) and the Online Mendelian Inheritance in Man database (OMIM). MutaGeneSys accepts SNP data of individuals as query input and delivers disease susceptibility hypotheses even if the original set of typed SNPs is incomplete. Our system produces population, genotyping technology, and confidence-specific predictions in interactive time.
The SEQERR program estimates the rate at which homozygous major allele genotypes are mis-called as heterozygote genotypes at low frequency markers. This error rate is estimated using observed allele and genotype frequencies at low frequency variants in identity by descent segments.
ADMIXMAP (Admixture mapping)is a general-purpose program for modelling admixture, using marker genotypes and trait data on a sample of individuals from an admixed population (such as African-Americans), where the markers have been chosen to have extreme differentials in allele frequencies between two or more of the ancestral populations between which admixture has occurred. The main difference between ADMIXMAP and classical programs for estimation of admixture such as ADMIX is that ADMIXMAP is based on a multilevel model for the distribution of individual admixture in the population and the stochastic variation of ancestry on hybrid chromosomes. This makes it possible to model the associations of ancestry between linked marker loci, and the association of a trait with individual admixture or with ancestry at a linked marker locus.
The Gigwa application provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also matching genotype patterns. It is a fairly lightweight, web-based, platform-independent solution that may be deployed on a workstation or as a data portal. It allows to feed a MongoDB database with VCF, PLINK or HapMap files containing up to tens of billions of genotypes, and provides a user-friendly interface to filter data in real time.
CNGen is a scritp that converts integrated SNP and CNV calls generated from Birdsuite ‘s Fawkes procedure into phased copy number genotypes (CN genotypes) using familial pedigree data. This software makes possible the use of CNPs and CNVs for genetic linkage with family data.
MULTIPRED2 is a computational system for large-scale screening of peptide binding to multiple alleles belonging to human leukocyte antigen (HLA) class I and class II DR supertypes as well as to alleles belonging to an individual’s genotype.
ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.