This directory contains zipped multiple alignments of the 
human (hg17, May 2004) and mouse (mm5, May 2004) assemblies 
to the dog (canFam1, Jul. 2004) assembly. The chr*.maf.gz 
files each contain all the alignments to that particular 
dog chromosome.  

The hg17 and mm5 directories contained gzipped alignment files 
for the pairwise (blastz) alignments used in the multiple alignment.

For a description of multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html.

If you plan to download a large file or multiple files from 
this directory, we recommend that 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/canFam1/multizHg17Mm5/. 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 usable for any 
purpose.

The dog genome sequence is made freely available by the Dog Genome Sequencing
Project. Please cite the following publication when using these data:

Lindblad-Toh K, et al. Genome sequence, comparative analysis and haplotype
structure of the domestic dog. Nature. 2005 Dec 8;438:803-19.