Pedigree reconstruction software tools | Population genetics data analysis
The problem of inference of family trees, or pedigree reconstruction, for a group of individuals is a fundamental problem in genetics. Various methods have been proposed to automate the process of pedigree reconstruction given the genotypes or haplotypes of a set of individuals.
Performs paternity assignment using likelihood. Cervus determines allele frequencies, performs simulations and analysis paternity in study populations, as well as identity analysis, starting with text-based genetic data. The software can process datasets that contain many thousands of loci. It permits users to determine parent-offspring relationships, including when some genotypes are incomplete, incorrect or missing. Cervus was used to analyze paternity in Rum red deer.
Offers a method for association-detection testing of samples with related individuals from structured populations. ROADTRIPS is able to correct pedigree and population structure thanks to a covariance matrix, including admixture. It includes features for handling missing data, for including either unaffected controls and controls of unknown phenotype into the process. This tool is able to deliver an enriched analysis by incorporating data about pedigree structure of the sampled individuals.
Infers the most likely relationship of a pair of putative sibs. RELPER consider all possible pairs of individuals in the sample, to test for additional relationships, to allow explicitly for genotyping error, and to include X-linked data. Using autosomal genome scan data, our method has excellent power to differentiate monozygotic twins, full sibs, parent-offspring pairs, second-degree (27) relatives, first cousins, and unrelated pairs but is unable to distinguish accurately among the 27 relationships of half sibs, avuncular pairs, and grandparent-grandchild pairs.
A program for cutting complex pedigree into computable sub-pedigrees with user-specified MaxBit size. PedCut recursively groups the subjects of interest (SOI) into subgroups that fall within a certain bitsize limit and include the maximum number of SOI who share a common ancestor. We developed a heuristic algorithm that is suitable to split large and complex pedigrees coming from genetically isolated populations.
Detects pedigree errors, cryptic relatedness and relationship mispecification in genome-wide association study (GWAS) or linkage data. Using an optimized maximum likelihood estimation (MLE) estimator for identity by descent (IBD) probabilities, prest-plus computes accurate estimates for IBD0/1/2 using any number and combination of single nucleotide polymorphism (SNP) or microsatellite marker data. It can work as efficiently and accurately with a microsatellite linkage panel or SNP data from a GWAS study.
An automatic heuristic algorithm for pedigree splitting, facilitating the use of the resulting subpedigrees for haplotyping, identical-by-descent (IBD) computation or multipoint linkage analysis. PedStr specifically aims to split large pedigrees where many close relatives are genotyped and phenotyped. Within a user-defined bit size limit the algorithm identifies subpedigrees having the maximal total relationship between individuals of interest. It produces a set of subpedigrees for IBD computation, multipoint linkage analysis or haplotype reconstruction with the help of the Lander-Green-Kruglyak algorithm. Our algorithm is useful for IBD-based multipoint linkage analysis of quantitative traits. It ensures significantly higher linkage power than the alternative algorithm Jenti and significantly smaller running time than the alternative algorithm PedCut.
Assists users in detecting pedigree errors. GRR graphically inspects the distribution for marker allele sharing among pairs of family members or all pairs of individuals in a study. This Windows application is able to display sib pairs, half sibs, parent-offspring pairs, and unrelated pairs. The user can select which pairings are to be displayed.