This directory contains reciprocal-best netted chains for caeRem4-panRed1.

 - caeRem4.panRed1.rbest.net.gz: caeRem4-referenced recip.best net to panRed1.
 - caeRem4.panRed1.rbest.chain.gz: chains extracted from the recip.best
   net.  These can be passed to the liftOver program to translate coords
   from caeRem4 to panRed1 through the recip.best net.

 - panRed1.caeRem4.rbest.net.gz: panRed1-referenced recip.best net.
 - panRed1.caeRem4.rbest.chain.gz: recip.best "liftOver" chains.

 - axtRBestNet/caeRem4.panRed1.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