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Pedigree reconstruction software tools | Whole-genome sequencing 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…
Prest-plus
Desktop

Prest-plus

Detects pedigree errors, cryptic relatedness and relationship mispecification…

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…

hsphase
Desktop

hsphase

Exploits the genetic structure found in half-sib livestock data to identify and…

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…

FRANz
Desktop

FRANz

A package for pedigree reconstruction in natural populations using co-dominant…

A package for pedigree reconstruction in natural populations using co-dominant genomic markers such as microsatellites and single nucleotide polymorphisms (SNPs). FRANz makes use of prior information…

RELPAIR
Desktop

RELPAIR

Infers the most likely relationship of a pair of putative sibs. RELPER consider…

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…

KinLinks
Desktop

KinLinks

Predicts pairwise kinship degree predictions. KinLinks builds training models…

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,…

CARROT
Desktop

CARROT ClAssification of Relationships with ROTations

Leverages linkage information to differentiate between rotated relationships.…

Leverages linkage information to differentiate between rotated relationships. CARROT uses a novel heuristic to decide whether one of the two individuals under consideration is closer to the common…

PedCut
Desktop

PedCut

A program for cutting complex pedigree into computable sub-pedigrees with…

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…

IPED
Algorithm

IPED Inheritance Path-based PEDigree reconstruction

Reconstructs very large pedigrees. IPED software is designed to handle complex…

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…

PedStr
Desktop

PedStr Pedigree Strip

An automatic heuristic algorithm for pedigree splitting, facilitating the use…

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.…

PedPeel
Desktop

PedPeel

A graph theoretic algorithm for optimal selection of peeling order in zero-loop…

A graph theoretic algorithm for optimal selection of peeling order in zero-loop pedigrees with incomplete genotypic information. PedPeel can be easily introduced into the existing software packages…

Famsphere
Desktop

Famsphere

Allocates families based on microsatellite marker information. Famsphere…

Allocates families based on microsatellite marker information. Famsphere formalizes the exclusion method considering genotyping errors or mutations. It provides a way to resolve conflicts in the case…

PedAgree
Desktop

PedAgree

Compares output from seven sibship reconstruction (SR) and thirteen parentage…

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…

PAPA
Desktop

PAPA Package for the Analysis of Parental Allocation

Simulates and allocates parental pair. PAPA is based on the likelihood of a…

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…

PASOS
Desktop

PASOS Parental Allocation of Singles in Open Systems

Identifies collected parents based on individual multilocus genotypes while…

Identifies collected parents based on individual multilocus genotypes while detecting missing parents when a proportion of them have not been collected. PASOS combines an approach based on parental…

Probmax
Desktop

Probmax

Helps researchers to identify the parents of an individual sampled from a…

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.…

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