This directory contains reciprocal-best netted chains for braFlo1-mm9.

 - braFlo1.mm9.rbest.net.gz: braFlo1-referenced recip.best net to mm9.
 - braFlo1.mm9.rbest.chain.gz: chains extracted from the recip.best
   net.  These can be passed to the liftOver program to translate coords
   from braFlo1 to mm9 through the recip.best net.

 - mm9.braFlo1.rbest.net.gz: mm9-referenced recip.best net.
 - mm9.braFlo1.rbest.chain.gz: recip.best "liftOver" chains.
 - Checksum values for all files in this directory can be found in md5sum.txt.

 - axtRBestNet/chr*.braFlo1.mm9.rbest.axt.gz: chained and netted alignments,
   i.e. the best chains in the Lancelet genome, with gaps in the best
   chains filled in by next-best chains where possible.  Only alignments
   that are reciprocal best are kept.  The axt format is
   described in http://genome.ucsc.edu/goldenPath/help/axt.html .