This directory contains reciprocal-best netted chains for ce11-caeJap4.

 - ce11.caeJap4.rbest.net.gz: ce11-referenced recip.best net to caeJap4.
 - ce11.caeJap4.rbest.chain.gz: chains extracted from the recip.best
   net.  These can be passed to the liftOver program to translate coords
   from ce11 to caeJap4 through the recip.best net.

 - caeJap4.ce11.rbest.net.gz: caeJap4-referenced recip.best net.
 - caeJap4.ce11.rbest.chain.gz: recip.best "liftOver" chains.

 - axtRBestNet/*.ce11.caeJap4.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