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.
TASSEL (Trait Analysis by aSSociation, Evolution, and Linkage) is a software package which performs a variety of genetic analyses. The analyses include association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information.
rTASSEL construct an R-based front-end to connect to a variety of highly used TASSEL methods and analytical tools.
LHiSA is an algorithm dedicated to large-scale association studies which aims to identify segments of genome involved in a disease. It is based on Local Score statistic and an automatic selection of the significant segments.
MultAssoc is a MATLAB software package for test of association of a disease with a group of SNPs after accounting for their interaction with another group of SNPs or environmental exposures. In addition to implementing two standard logistic regression based tests, the package implements a novel method, called TukAssoc, that uses the Tukey’s 1 d.f. model for interaction between two groups of covariates.
The GIST (Genotype-IBD Sharing Test) is a method for detecting association between marker genotypes and IBD sharing at the same locus. Such an association will indicate that the marker itself, or one in linkage disequilibrium with it, could account for the observed linkage signal (at least partially). The software can be used to analyze affected sibship data.
PAINTOR (Probabilistic Annotation INtegraTOR) is a probabilistic framework that integrates association strength with genomic functional annotation data to improve accuracy in selecting plausible causal variants for functional validation.
BaTS (Bayesian Tip-Significance testing) is a package that allows the user to test for significant phylogeny-trait correlations whilst taking into account uncertainty arising from phylogenetic error, by integrating over the credible set of topologies produced by Bayesian phylogenetics programs such as BEAST or MrBayes. Null distributions are generated for statistics of phylogeny-trait association, and used to test the significance of the observed data. BaTS can also perform batch analyses of multiple data sets.
MT-HESS is a Bayesain hierarchical model that analyses the association between a large set of predictors, e.g. SNPs (single nucleotide polymorphisms), and many responses, e.g. gene expression, in multiple tissues, cells or conditions.
The RVFam package provides functions to perform single SNP association analyses and gene-based tests for continuous, binary and survival traits against sequencing data (e.g. exome chip) using family data.