This directory contains reciprocal-best netted chains for canFam3-mm9.

 - canFam3.mm9.rbest.net.gz: canFam3-referenced recip.best net to mm9.
 - canFam3.mm9.rbest.chain.gz: chains extracted from the recip.best
   net.  These can be passed to the liftOver program to translate coords
   from canFam3 to mm9 through the recip.best net.

 - mm9.canFam3.rbest.net.gz: mm9-referenced recip.best net.
 - mm9.canFam3.rbest.chain.gz: recip.best "liftOver" chains.

 - axtRBestNet/canFam3.mm9.rbest.axt.gz reciprocal best alignments in
   AXT format

See also, description of AXT format::
    http://genome.ucsc.edu/goldenPath/help/axt.html
description of CHAIN format:
    http://genome.ucsc.edu/goldenPath/help/chain.html
description of NET format:
    http://genome.ucsc.edu/goldenPath/help/net.html