This directory contains compressed phastCons scores for multiple
alignments of 4 other vertebrate genomes to the cow genome:

  - cow             Bos taurus              Oct 2007, bosTau4  reference
  - dog             Canis familiaris        May 2005, canFam2  syntenic net
  - human           Homo sapiens            Mar 2006, hg18     syntenic net
  - mouse           Mus musculus            July 2007, mm9     syntenic net
  - platypus        Ornithorhychus anatinus Mar 2007, ornAna1  syntenic net

Files in this directory are:
    5way.mod      phastCons tree model with branch lengths for the 5 species
    file_*.data.gz - phastCons scores for the 5 species
	each file contains the data for a number of chromosomes or
	the chrUn contigs for the Cow genome

The multiple alignments and methods description are at:

For a description of the phastCons file format, see

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: 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/bosTau4/phastCons5way

To download multiple files from the UNIX command line, use the "mget" command. 
    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 
Use the "prompt" command to toggle the interactive mode if you do not want 
to be prompted for each file that you download.

All the files in this directory are freely available for public use.
For data use restrictions regarding the genome assemblies used in this
annotation, see

References for phastCons:

Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A., Hou, M., 
Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S., 
Weinstock, G.M., Wilson, R. K., Gibbs, R.A., Kent, W.J., Miller, W., 
and Haussler, D.  Evolutionarily conserved elements in vertebrate, insect, 
worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).

Siepel, A. and Haussler, D. Phylogenetic hidden Markov models.
In R. Nielsen, ed., Statistical Methods in Molecular Evolution,
Springer (in press) (2004).
      Name                    Last modified      Size  Description
Parent Directory - md5sum.txt 2008-03-28 13:33 288 5way.mod 2008-03-19 10:11 418 2008-03-19 12:09 34K 2008-03-19 12:09 1.3M 2008-03-19 12:09 3.0M 2008-03-19 12:09 11M 2008-03-19 12:09 1.9G