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.
CYNTENATOR is a progressive gene order alignment software to identify genomic regions of conserved synteny over a large set of diverging species. CYNTENATOR does not depend on nucleotide-level alignments and a priori homology assignment.
The software package CDS-plotcon is specifically designed to search for conserved functional elements within CDSs. It uses an average model of the expected mutation patterns within CDSs (incorporating a nucleotide mutation matrix, amino acid substitution matrix, sequence divergence parameter t, mean synonymous:nonsynonymous substitution ratio V and phylogenetic tree; it can handle up to three overlapping CDSs in different read-frames). Using this, it calculates the expected number of mutations across the alignment in each column and compares this with the observed number of mutations. The results are plotted along the genome, and optionally passed through a sliding window (clipped) mean filter
ATOM is a software of powerful gene-based Association Test by combining Optimally Weighted Markers within a genomic region. Due to variation in linkage disequilibrium, different markers often associate with the trait of interest at different levels.
SampleSeq is a probability-based algorithm for selecting samples for a targeted resequencing experiment.
SampleSeq2 requires a squared matrix of pairwise distance among all subjects that are candidates for selection. The matrix can be generated by PLINK using GWAS data or by Idcoefs using pedigree information. These are explained in detail in Sections II and III.In Section IV, we describe how to use SampleSeq2 for subject selection. In Section V, we describe how to estimate the number of independent genomes in a subset of subjects.
GWAsimulator is a C++ program that can simulate genotype data for SNP chips that are used in genome-wide association (GWA) studies. It implements a rapid moving-window algorithm (Durrant et al. 2004. AJHG 75:35-43) to simulate whole genome case-control or population samples. It also can simulate specific regions if desired. For case-control data, the program retrospectively sample cases and controls according to a user-specified multi-locus disease model. The program requires phased data as input, and the simulated data will have similar LD patterns as the input data.