This directory contains compressed phastCons scores for multiple
alignments of 5 other nematode genomes to the C. elegans genome:

  - C. elegans      May 2008, ce6          reference
  - C. remanei      May 2007, caeRem3      chain net
  - C. briggsae     Jan 2007, cb3          chain net
  - C. brenneri     Feb 2008, caePb1       chain net
  - C. japonica     Mar 2008, caeJap1      chain net
  - P. pacificus    May 2007, priPac1      chain net

Files in this directory are:
    6way.conserved.mod      phastCons conserved tree model 
    6way.non-conserved.mod  phastCons non-conserved tree model
    chr*.data.gz - phastCons scores for the 6 species
    md5sum.txt - MD5 check sums for the *.data.gz and *.mod files

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/ce6/phastCons6way

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 - 6way.conserved.mod 2008-06-18 11:40 444 6way.non-conserved.mod 2008-06-18 11:40 444 2008-06-18 11:59 14M 2008-06-18 12:00 14M 2008-06-18 12:00 13M 2008-06-18 12:00 15M 2008-06-18 12:00 18K 2008-06-18 12:00 20M 2008-06-18 12:00 18M md5sum.txt 2008-06-23 14:59 443