This directory contain chimp/human alignments made
using the Nov 2003 Arachne chimp assembly (NCBI Build 1 Version 1)
vs. the Human July 2003 human assembly (also known as UCSC hg16  or NCBI
Human Build 34). 

The subdirectory netChain contains chain files extracted
from the human net alignment track, giving a "best-in-genome"
set of alignments.  The chain file format is described in the 
file chainFormat.doc

For more information on the chain and net algorithms, 
see the Methods section of the description pages associated with the net
 and chain tracks.