This program compares a genetic linkage map with a genome assembly and highlights locus positions that that disagree between them.  “Given a discription of an assembly, and a description of a genetic map, Chromonomer will try to reconcile them”

This approach could also be useful to compare our linkage maps of Pacific salmon species to published genomes in O. mykiss and S. Salar.

Software available at:

http://catchenlab.life.illinois.edu/chromonomer/

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