This directory contains reciprocal-best netted chains for susScr3-mm39.

 - susScr3.mm39.rbest.net.gz: susScr3-referenced recip.best net to mm39.
 - susScr3.mm39.rbest.chain.gz: chains extracted from the recip.best
   net.  These can be passed to the liftOver program to translate coords
   from susScr3 to mm39 through the recip.best net.

 - mm39.susScr3.rbest.net.gz: mm39-referenced recip.best net.
 - mm39.susScr3.rbest.chain.gz: recip.best "liftOver" chains.

 - axtRBestNet/susScr3.mm39.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