This directory contains compressed phastCons scores for multiple
alignments of 7 vertebrate genomes to the orangutan genome:

    - orangutan       Pan troglodytes         July 2007, ponAbe2
    - human           Homo sapiens            Mar 2006, hg18
    - chimpanzee      Pan troglodytes         Mar 2006, panTro2
    - rhesus          Macaca mulatta          Jan 2006, rheMac2
    - marmoset        Callithrix jacchus      June 2007, calJac1
    - mouse           Mus musculus            July 2007, mm9
    - opossum         Monodelphis domestica   Jan 2006, monDom4
    - platypus        Ornithorhychus anatinus Mar 2007, ornAna1

Files in this directory are:
    8way.mod      phastCons tree model with branch lengths for the 8 species
    phastConsScores/*.data.gz - phastCons scores for 8 species

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/ponAbe2/phastCons8way

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 - 8way.mod 2007-12-03 14:13 502 phastConsScores/ 2007-12-27 13:23 -