This directory contains compressed phastCons scores for multiple
alignments of the following yeasts to the Saccharomyces cerevisiae 
genome (sacCer2):
- Saccharomyces paradoxus
- Saccharomyces mikatae
- Saccharomyces kudriavzevii
- Saccharomyces bayanus
- Saccharomyces castelli
- Saccharomyces kluyveri

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/multiz7way/README.txt

For a description of the phastCons file format, see
http://genome.ucsc.edu/goldenPath/help/phastCons.html.

These alignments were prepared using the methods described in the
track description file:
http://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/multiz7way/multiz7way.html,
based on the phylogenetic tree:
http://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/multiz7way/7way.nh

PhastCons was operated with the command:

phastCons - ave.cons.mod,ave.noncons.mod --expected-lengths 75 \
    --target-coverage 0.5 --quiet --seqname chrN --idpref chrN \
        --viterbi ELEMENTS/chrN.bed --score --require-informative 0 \
	| gzip > chrN.pp.gz

Note the two model files here:
	ave.cons.mod and ave.noncons.mod

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If you plan to download a large file or multiple files from this 
directory, we recommend 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/sacCer2/phastCons7way. To download multiple files, 
use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory)

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 http://genome.ucsc.edu/goldenPath/credits.html.

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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).
(http://www.genome.org/cgi/doi/10.1101/gr.3715005)

Siepel, A. and Haussler, D. Phylogenetic hidden Markov models.
In R. Nielsen, ed., Statistical Methods in Molecular Evolution,
Springer (in press) (2004).

For a discussion of the methods used to calculate the phastCons scores,
see the description page for the sacCer2 Conservation track in the Genome
Browser.