This directory contains human/chimpanzee "reciprocal best" alignments 
in chromosome coordinates using the 13 Nov. 2003 Arachne 4x draft
chimp assembly from the Broad Institute, MIT/Harvard, with sequence 
provided by the Broad Institute and Washington University, St. Louis, 
and chromosome mapping provided by LaDeana Hillier at Washingon 
University. The Chimpanzee Genome Sequencing project is sponsored by
NHGRI.

Files included in this directory:

 - axtRBestNet: axt reciprocal best alignment files

 - chainFormat.txt: description of chain file format

 - human.best.chain.gz: human-reference chains

 - md5sum.txt: checksum file

For a description of the chain file format, see
http://genome.ucsc.edu/goldenPath/help/chain.html.

For more information on these alignments and the chain and net algorithms,
see the Methods section of the description pages associated with the 
Human July 2003 browser Chimp Net and Chimp Chain tracks.

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If you plan to download a large file or multiple files from this 
directory, we recommend you use ftp rather than downloading the files 
via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to 
the directory goldenPath/hg16/vsPanTro1/. To download multiple 
files, use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 

All the files in this directory are freely available for public use.