This directory contains reciprocal-best netted chains for petMar1-hg18. - petMar1.hg18.rbest.net.gz: petMar1-referenced recip.best net to hg18. - petMar1.hg18.rbest.chain.gz: chains extracted from the recip.best net. These can be passed to the liftOver program to translate coords from petMar1 to hg18 through the recip.best net. - hg18.petMar1.rbest.net.gz: hg18-referenced recip.best net. - hg18.petMar1.rbest.chain.gz: recip.best "liftOver" chains. - Checksum values for all files in this directory can be found in md5sum.txt. - axtRBestNet/petMar1.hg18.rbest.axt.gz: chained and netted alignments, i.e. the best chains in the Lamprey 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 .