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http://www.atgc.org/XLinkage/MadMapper/
Suite of Python scripts for quality control of genetic markers, group analysis and inference of linear order of markers on linkage groups. MadMapper_RECBIT analyses raw marker scores for recombinant inbred lines. MadMapper_RECBIT generates pairwise distance scores for all markers, clusters based on pairwise distances, identifies genetic bins, assigns new markers to known linkage groups, validates allele calls, and assigns quality classes to each marker based on several criteria and cutoff values. MadMapper_XDELTA utilizes new algorithm, Minimum Entropy Approach and Best-Fit Extension, to infer linear order of markers. MadMapper_XDELTA analyzes two-dimensional matrices of all pairwise scores and finds best map that has minimal total sum of differences between adjacent cells (map with lowest entropy). MadMapper is freely available at http://www.atgc.org/XLinkage/MadMapper/ (entry from Genetic Analysis Software)
Proper citation: MADMAPPER (RRID:SCR_009267) Copy
http://www.hsph.harvard.edu/faculty/alkes-price/software/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. A software suite designed to more powerfully leverage clinical-covariates such as age, bmi, smoking status, and gender when conducting case-control association studies. Including these covariates in standard regression models is not only suboptimal, but can in many instances reduce power. LTSOFT employs a liability threshold model approach that takes advantage of known epidemiological results to better model the covariates'' relationship to the phenotype of interest (entry from Genetic Analysis Software)
Proper citation: LTSOFT (RRID:SCR_009266) Copy
https://github.com/gaow/genetic-analysis-software/blob/master/pages/LRP.md
Software application that is part of the LINKAGE auxiliary program (entry from Genetic Analysis Software)
Proper citation: LRP (RRID:SCR_009263) Copy
http://statgen.iop.kcl.ac.uk/lpop/
Software application that detects population stratification in samples of unrelated individuals for whom a number of unlinked genotypes have been measured. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: L-POP (RRID:SCR_009262) Copy
http://www.stat.washington.edu/thompson/Genepi/Loki.shtml
Software program for analyses a quantitative trait observed on large pedigrees using Markov chain Monte Carlo multipoint linkage and segregation analysis. The trait may be determined by multiple loci. (entry from Genetic Analysis Software)
Proper citation: LOKI (RRID:SCR_009260) Copy
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