This directory contain chimpanzee/human alignments made using the 
Nov 2003 Arachne chimp assembly (NCBI Build 1 Version 1, UCSC panTro1)
vs. the Human May 2004 human assembly (NCBI Human Build 35, UCSC hg17). 

The axtNet directory contains alignments indicating the best chimp/human 
chain for every part of the human genome. For more information on the 
algorithms used to generate these alignments, see the Methods section of 
the Human Chain and Human Net tracks in the chimpanzee browser.

The alignments are in "axt" format. For a description, see 
http://genome.ucsc.edu/goldenPath/help/axt.html.