This directory contains human/chimpanzee "reciprocal best" alignments 
made 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.
The Chimpanzee Genome Sequencing project was sponsored by
NHGRI.

Files in this directory include:

 - chimp.best.chain.gz: chimp-reference chains
 - human.best.chain.gz: human-reference chains
 - scaffolds.msk.fa.gz: masked sequence supercontigs
 - md5sum.txt: checksum file
 - chainFormat.txt: description of chain file format

For more information on the chain file format, see
http://genome.ucsc.edu/goldenPath/help/chain.html.

The scaffolds file contains sequence soft-masked by RepeatMasker,
using the standard primate library, and default settings, with
additional masking by Tandem Repeat Finder.

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/vsPt0/. To download multiple 
files, use the "mget" command:

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

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