LAMP (Linkage & Association Modeling for Pedigrees) uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees (Li et al, 2005; Li et al, 2006). It provides estimates of genetic model parameters and powerful tests of association in settings where population stratification is not a concern.
COCACOLA is a general framework that combines different types of information: sequence COmposition, CoverAge across multiple samples, CO-alignment to reference genomes and paired-end reads LinkAge to automatically bin contigs into OTUs.
SIMLA (SIMulation of pedigree data for Linkage and Association studies) is a SIMulation program that generates data sets of families for use in Linkage and Association studies. It allows the user flexibility in specifying marker and disease placement, locus heterogeneity, disequilibrium between markers and between markers and disease loci. Output is in the form of a LINKAGE pedigree file and is easily utilized, either directly or with minimal reformatting, as input for various genetic analysis packages.
MFLINK is a simple program which automates setting up likelihood calculations for linkage analysis using a variety of different transmission models, and then collating the results in order to produce a (nearly) model free lod score.
PSEUDOMARKER is linkage analysis software for joint Linkage and LD analysis for qualitative traits. Pseudomarker can analyze different data structures jointly such as cases and controls, trios, sib pairs, sib ships and extended families. Pseudomarker is family-based association test.
LINKAGE package is a series of programs for maximum likelihood estimation of recombination rates, calculation of lod score tables, and analysis of genetic risks. The analysis programs are divided into two groups. The first group can be used for general pedigrees with marker and disease loci. Programs in the second group are for three-generation families and codominant marker loci, and are primarily intended for the construction of genetic maps from data on reference families.
Linkdatagen is a PERL script that generates LINKAGE style files for ALLEGRO , MERLIN, PREST, MORGAN, PLINK, FEstim, BEAGLE and RELATE using as input genotype calls from Affymetrix SNP chips, Illumina SNP chips, or SNP genotypes inferred from massively parallel sequencing (MPS) data, such as whole exome or whole genome sequence data.