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IPED / Inheritance Path-based PEDigree reconstruction
Reconstructs very large pedigrees. IPED software is designed to handle complex pedigrees and is particularly designed to handle inbreeding and the presence of half-siblings. Also, it reconstructs pedigree only from the extant individuals. When the genotypes of the internal individuals are known, it is helpful to use all such information. For each generation, it predicts the pairwise relationships between the individuals at the current generation and creates parents for them according to their relationships.
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.
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.
Exploits the genetic structure found in half-sib livestock data to identify and count recombination events, impute and phase un-genotyped sires and phase its offspring. hsphase also allows reconstruction of family groups (pedigree inference), identification of pedigree errors and parentage assignment. Additional functions in the package allow identification of genomic mapping errors, imputation of paternal high density genotypes from low density genotypes, evaluation of phasing results either from hsphase or from other phasing programs.
PAPA / Package for the Analysis of Parental Allocation
Simulates and allocates parental pair. PAPA is based on the likelihood of a parental pair producing the multilocus genotype found in the offspring being tested. It is basically a parental pair allocation program so it differs from paternity/maternity allocations programs. The tool provides a Monte-Carlo simulator that may be used to obtain empirical distributions of many relevant random variables such as rates of successful allocations and allocation failures.
Helps researchers to identify the parents of an individual sampled from a population mixture when the genetic variation at several loci is known in both the progeny mixture and in the parents. PROBMAX allows the user to generate random progeny genotypic sets from the cross-combinations and genotypes. It could be helpful in determining whether the specified number of genetic markers being tested will be able to discriminate the exact parentage of the progeny in the pool being examined or whether additional markers may be needed to fulfil this objective.
PedStr / Pedigree Strip
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.
Compares output from seven sibship reconstruction (SR) and thirteen parentage assignment programs to known pedigrees for accuracy assessment, and to one another for congruence. PedAgree is software for rapid comparison of genetically reconstructed pedigrees (RP’s). Its two primary functions are (i) to assess accuracy of a RP by comparing it to a known pedigree, and (ii) to measure congruence between two RP’s. It was developed to assist with accuracy improvement and assessment. It is used for two primary functions: to assess accuracy and quantify error, and to assess output congruence.
Predicts pairwise kinship degree predictions. KinLinks builds training models to proceed. It combines some of the standard approaches to kinship prediction such as the Kinship Coefficient, probability of zero identity by state, and likelihood ratio calculation. The tool can identify the most likely pedigree from multiple candidates to predict pairwise kinship relationships and automatically reconstruct pedigrees for multiple single nucleotide polymorphism (SNP) genotyped samples.
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