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. Author manuscript; available in PMC: 2015 May 21.
Published in final edited form as: Nat Rev Genet. 2015 Mar 31;16(5):275–284. doi: 10.1038/nrg3908

Table 1. Computer implementations.

Software Description and purpose URL Refs
easyLINKAGE Integrated suite that generates the necessary files and performs analysis using several programs, including GeneHunter http://sourceforge.net/projects/easylinkage/ 92
Genome Analysis Toolkit (GATK) Toolkit for call variants from WGS data https://www.broadinstitute.org/gatk/ 81
GeneHunter

  • Lander–Green algorithm

  • Can be applied to small- to medium-sized families and large numbers of marker loci

  • Features parametric and non-parametric multipoint linkage analysis for qualitative and quantitative traits

 http://www.broadinstitute.org/ftp/distribution/software/genehunter/ 46
GIGI-Check

  • MCMC algorithm

  • Detects Mendelian-consistent genotyping errors

 https://faculty.washington.edu/wijsman/progdists/gigi/software/GIGI-Check/GIGI-Check.html 86
GIGI-Pick Can be used to prioritize individuals for WGS https://faculty.washington.edu/wijsman/progdists/gigi/software/GIGI-Pick/GIGI-Pick.html 42
LINKAGE and FASTLINK

  • Elston–Stewart algorithm

  • Can be applied to large families but only to a limited number of marker loci for multipoint, parametric two-point and parametric multipoint linkage analysis for qualitative and quantitative traits

  • Can be used to detect Mendelian-consistent genotyping errors

 http://www.jurgott.org/linkage/LinkagePC.html; http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/fastlink.html 44, 93
Loki

  • MCMC algorithm

  • Can be used to perform multipoint linkage and segregation analysis of quantitative traits on large pedigrees

 http://www.stat.washington.edu/thompson/Genepi/Loki.shtml 94
Mendel

  • Elston–Stewart and Lander–Green algorithms

  • Can be applied to the analysis of qualitative or quantitative traits in pedigree- or population-based data

  • Can combine multiple (rare) variants into superloci

 http://www.genetics.ucla.edu/software/mendel 95, 96
MERLIN

  • Lander–Green algorithm

  • Can be applied to small- to medium-sized pedigrees

  • Handles closely spaced SNPs by combining them into superloci

 http://www.sph.umich.edu/csg/abecasis/Merlin/ 47
MSIM

  • Elston–Stewart algorithm

  • Can be used to analyse simulated pedigree data to evaluate power, maximum LOD scores and expected LOD scores

  • Useful for simulation studies to evaluate the most-informative pedigree members to select for WGS

 http://watson.hgen.pitt.edu/docs/SLink.html 97
PedCheck Detects genotype incompatibilities in pedigree data http://watson.hgen.pitt.edu/register/docs/pedcheck.html 98
PLINK

  • Whole-genome association tool set for genotype data

  • Can be used to estimate IBD sharing between two individuals

 http://pngu.mgh.harvard. edu/∼purcell/plink/ 48
Pseudomarker

  • Family-based association testing (joint linkage and linkage analysis) for qualitative traits using cases and controls, trios, sibpairs, sibships and extended families

 http://www.helsinki.fi/∼tsjuntun/pseudomarker/ 99
SEQLinkage

  • Elston–Stewart algorithm

  • Can be used for parametric linkage analysis of WGS data using the collapsed haplotype pattern method

  • Generates linkage files from VCF files for use with any linkage program that performs parametric linkage analysis

 http://bioinformatics.org/seqlink 51
SimWalk2

  • MCMC algorithm

  • Can handle large pedigrees and an intermediate number of marker loci for parametric and non-parametric multipoint linkage analysis of qualitative and quantitative traits

 http://www.genetics.ucla.edu/software/ 54
SLINK and FastSLINK

  • Simulates pedigree data that are conditional and unconditional on qualitative and quantitative phenotypes

  • Limited in size of pedigree and number of marker loci

  • MSIM can be used to analyse the simulated pedigrees

 http://watson.hgen.pitt.edu/docs/SLink.html 97
Superlink

  • Bayesian networks

  • Can handle large, complex pedigrees with multiple inbreeding loops segregating dichotomous traits

  • Performs two-point and multipoint (with a limited number of markers) linkage analysis

 http://bioinfo.cs.technion.ac.il/superlink/ 100
TLINKAGE

  • Elston–Stewart algorithm

  • Can handle large pedigrees

  • Performs parametric two-locus linkage analysis

 http://www.jurgott.org/linkage/tlinkage.htm 63
Variant Association Tools (VAT)

  • Pipeline for quality control and analysis of WGS and genotype data

  • Can be used to generate linkage files for VCF files and to estimate IBD sharing between a pair of individuals

 http://varianttools.sourceforge.net/VAT 50
VCFtools Program to manipulate VCF files http://vcftools.sourceforge.net/ 49

IBD, identity-by-descent; MCMC, Markov-chain Monte Carlo; SNP, single-nucleotide polymorphism; VCF, Variant Cell Format; WGS, whole-genome sequencing.