This directory contains reciprocal-best netted chains for mm39-tupBel1.

 - mm39.tupBel1.rbest.net.gz: mm39-referenced recip.best net to tupBel1.
 - mm39.tupBel1.rbest.chain.gz: chains extracted from the recip.best
   net.  These can be passed to the liftOver program to translate coords
   from mm39 to tupBel1 through the recip.best net.

 - tupBel1.mm39.rbest.net.gz: tupBel1-referenced recip.best net.
 - tupBel1.mm39.rbest.chain.gz: recip.best "liftOver" chains.

 - axtRBestNet/*.mm39.tupBel1.net.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