Pgltools is a genomic arithmetic software suite designed for working with paired-loci genomic data, such as contacts from a Hi-C or ChIA-PET experiment, and utilizes the PGL file format.
Locusmap is a computer package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. The current version offers linkage analysis between codominant loci, between dominant loci, between codominant loci and dominant loci, and between codominant and sex-influenced, sex-linked, and imprinted loci. Using genotypic data supplied by the user, Locusmap calculates two-point recombination frequencies and LOD scores and then identifies linkage groups and orders loci within each linkage group automatically. Locusmap checks for genotypic and pedigree errors, and fills in missing genotypes when possible.
Mutation Reporter Tool (MRT) is an online tool which extracts and summarises nucleotide or amino acid sequence data at specified loci of interest. It is primarily aimed at researchers who want summarized distribution data of residue variation at known loci of interest.
LRASSOC suite deals with the situation where we have a case-control sample of affected and unaffected individuals with their marker genotypes for 2 biallelic marker loci. These 2 marker loci may be in linkage disequilibrium with 1 or 2 biallelic disease susceptibility loci and therefore affect disease risk through association or may themselves be disease susceptibility loci. We are interested in modelling the effects of the genotype on the probability of disease risk in order to draw conclusions regarding the nature of the joint effect of the loci. Among the issues we may wish to investigate are whether either of the 2 loci actually has an effect on disease risk, the strength and statistical significance of any effect, the nature of such an effect e.g is the effect additive on some scale or do the alleles at the same loci interact in a dominance effect. We also want to compare single and joint locus models to investigate how the strength and significance of the effect of each locus is affected by the presence or absence of the other in a model and, a related point, whether the additive and dominance effects of two loci are independent or whether they interact (often called epistasis in this context).
The Morgan2McClintock Translator permits prediction of meiotic pachytene chromosome map positions from recombination-based linkage data using recombination nodule frequency distributions.This tool uses the maize Recombination Nodule map (Anderson et al. 2003 and 2004) to calculate approximate chromosomal positions for loci given a genetic map for a single chromosome.
GRAIL is a tool to examine relationships between genes in different disease associated loci. Given several genomic regions or SNPs associated with a particular phenotype or disease, GRAIL looks for similarities in the published scientific text among the associated genes.
The VIZ-GRAIL software allows users to create informative circle plots of genetic loci that visualizes the functional similarites between genes in an intuitive manner. Code that interact with the online site is available here for download. VIZ-grail is implemented as two separate perl scripts.