HapYDive is a software for Y-STR haplotype diversity calculation.This program allows fast and reliable determination of which Y-STRs are the most informative by evaluating all possible combinations.With the HapYDive it is possible to analyse any set of Y markers up to a maximum of 20, with a minimum number of 4 markers fixed for calculations. Results on the application of this program to different population samples and sizes and with a certain combination of Y-STR markers are presented and discussed, together with its usefulness mainly to the forensic community.
RAIG ( Recurrent Aberrations from Interval Graph) is a combinatorial approach to the problem of identifying independent and recurrent copy number aberrations, focusing on the key challenging of separating the overlaps in aberrations across individuals into independent events.
Mosaic is a software which calculates the ‘mosaicity’ of a one dimensional hybrid zone. This package uses likelihood to fit step-wise models to one dimensional hybrid zone data, and to estimate the ‘mosaicity’ of the hybrid zone.
MQLS (More Powerful Quasi-Likelihood Score Test)can handle arbitrary number of markers and samples and have other features that we found useful in our studies, such as pedigree checking and input/output formats. In addition to genotyped markers, this version can carry out association tests using imputed allele counts (“dosages”) generated by MACH and an empirical variance estimator.
GSM (genetic similarity score matching)is a software for efficient matched analysis of cases and controls in a genome-wide or large-scale candidate gene association study. GSM comprises three steps: (1) calculating similarity scores for pairs of individuals using the genotype data; (2) matching sets of cases and controls based on the similarity scores so that matched cases and controls have similar genetic background; and (3) using conditional logistic regression to perform association tests. Through computer simulation we show that GSM correctly controls false-positive rates and improves power to detect true disease predisposing variants