MADMAPPER

Record added by Jurg Ott (the original Rockefeller list)

Version

September 2005

Description

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/

Author

Alexander Kozik (UC Davis Genome Center)

URL

http://www.atgc.org/XLinkage/MadMapper/

Language

Python

EXE

MadMapper_RECBIT, MadMapper_XDELTA