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Identity by descent (DNA-seq analysis)

Two haplotypes are identical by descent if they share the same alleles inherited from a common ancestor. Identity by descent (IBD) can be considered on various timescales. Emerging applications for the detected IBD segments include IBD mapping,…
GERMLINE
Desktop

GERMLINE

An algorithm for discovering long shared segments of Identity by Descent (IBD)…

An algorithm for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. GERMLINE takes as input genotype or haplotype marker data for…

BEAGLE…
Desktop

BEAGLE (fastIBD)

Performs genotype calling, genotype phasing, imputation of ungenotyped markers,…

Performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. FastIBD can be applied to thousands of samples across genome-wide SNP data…

Parente
Desktop

Parente

A method for detecting relatedness. It detects IBD accurately and rapidly using…

A method for detecting relatedness. It detects IBD accurately and rapidly using an embedded likelihood ratio test.

ngsF-HMM
Desktop

ngsF-HMM

A method for estimating inbreeding identity by descent (IBD) tracts from low…

A method for estimating inbreeding identity by descent (IBD) tracts from low coverage next-generation sequencing data. Contrary to other methods that use genotype data, the one presented here uses…

XIBD
Desktop

XIBD X chromosome Identity by Descent

Performs pairwise relatedness mapping on the X chromosome using dense single…

Performs pairwise relatedness mapping on the X chromosome using dense single nucleotide polymorphism (SNP) data from either SNP chips or next generation sequencing data. It correctly accounts for the…

IBD_Haplo
Desktop

IBD_Haplo

Inferring coancestry in population samples in the presence of linkage…

Inferring coancestry in population samples in the presence of linkage disequilibrium.

Relate
Desktop

Relate

This method estimates the probability of sharing alleles identity by descent…

This method estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals.

IBDLD
Desktop

IBDLD

A C++ program for multipoint IBD estimation based on high density SNP genotype…

A C++ program for multipoint IBD estimation based on high density SNP genotype data.

hmmIBD
Desktop

hmmIBD

Allows detection of genomic regions identical by decent (IBD) for pairs of…

Allows detection of genomic regions identical by decent (IBD) for pairs of haploid samples. hmmIBD uses simulated data, benchmarks it against a previously published method for detecting IBD within…

NgsRelate
Desktop

NgsRelate

A software tool for estimating pairwise relatedness from NGS data. NgsRelate…

A software tool for estimating pairwise relatedness from NGS data. NgsRelate provides maximum likelihood estimates that are based on genotype likelihoods instead of genotypes and thereby takes the…

IBDseq
Desktop

IBDseq

A software program for detecting segments of identity-by-descent (IBD) and…

A software program for detecting segments of identity-by-descent (IBD) and homozygosity-by-descent (HBD) in unphased genetic sequence data.

FISHR
Desktop

FISHR Find IBD Shared Haplotypes Rapidly

Detects IBD segments and estimates their endpoints using an algorithm that is…

Detects IBD segments and estimates their endpoints using an algorithm that is fast enough to be deployed on the very large whole-genome SNP datasets. We compared the performance of FISHR to three…

diCal-IBD
Desktop

diCal-IBD

A tool for detecting identity-by-descent (IBD) tracts between pairs of genomic…

A tool for detecting identity-by-descent (IBD) tracts between pairs of genomic sequences. This method builds on a recent demographic inference method based on the coalescent with recombination, and…

ENDOG
Desktop

ENDOG

Allows breeders and researchers to monitor changes in the genetic variability…

Allows breeders and researchers to monitor changes in the genetic variability and structure of the populations with limited cost of preparing datasets. ENDOG provides a number of features that may be…

PEDIBD
Desktop

PEDIBD PEDigree Identical-By-Descent

Reconstructs haplotypes in large families allowing many ungenotyped…

Reconstructs haplotypes in large families allowing many ungenotyped individuals. PEDIBD consists of three major steps: pairwise identical-by-descent (IBD) inference, global IBD reconstruction, and…

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