BIRCH - Genetics Software

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Mapmaker

Mapmaker is an interactive system for constructing genetic maps from molecular marker data for most types of genetic crosses.

Documentation:
Mapmaker Tutorial Adobe PDF (.pdf,  95k)   PostScript (.ps, 173k)
Mapmaker Reference Guide  Adobe PDF (.pdf,  83k)   PostScript (.ps, 259k)
MapmakerQTL  Tutorial Adobe PDF (.pdf,  87k)   PostScript (.ps, 165k)
MapmakerQTL  Reference Guide Adobe PDF (.pdf,  53k)   PostScript (.ps, 165k)
Data Preparation Guide, 19k
Sample datafiles

To run Mapmaker, type 'mapmaker'
To run MapmakerQTL, type 'qtl'

Mapmaker was developed by the Whitehead Institute for Biomedical Research and the MIT Center for Genome Research.

Genehunter

GENEHUNTER is a software package that allows the very rapid extraction of complete multipoint inheritance information from pedigrees of moderate size.  This information is then used in exact computation of multipoint LOD scores and in a powerful new method of non-parametric linkage analysis.  Quick calculations involving dozens of markers, even in pedigrees with inbreeding and marriage loops, is possible with GENEHUNTER.  In addition, the multipoint inheritance information allows the reconstruction of maximum-likelihood haplotypes for all individuals in the pedigree and information content mapping which measures the fraction of the total inheritance information extracted from the marker data.  All of these calculations are performed in a user-friendly environment familiar to MAPMAKER, SIBS, or HOMOZ users.

Documentation:
Genehunter Tutorial Adobe PDF (.pdf,  20k)   PostScript (.ps, 60k)
Sample datafiles

To run Genehunter for autosomal analysis, type 'gh'
To run Genehunter for X-chrromosomal analysis, type 'xgh'

Genehunter was developed by the Whitehead Institute for Biomedical Research and the MIT Center for Genome Research.

References:
L. Kruglyak, M.J. Daly, M.P. Reeve-Daly, and E.S. Lander. "Parametric and Nonparametric Linkage Analysis: A Unified Multipoint Approach".  American Journal of Human Genetics 58:1347-1363 (June 1996).

L. Kruglyak and E.S. Lander. "Faster Multipoint Linkage Analysis Using Fourier Transforms". Journal of Computational Biology 5:1-7 (1998).