This directory contains compressed phastCons scores for multiple
alignments of 5 other vertebrate genomes to the lancelet genome:

  - lancelet        Branchiostoma floridae  Mar 2006,  braFlo1  reference
  - human           Homo sapiens            Mar 2006,  hg18     recip best net
  - mouse           Mus musculus            July 2007, mm9      recip best net
  - chicken         Gallus gallus           May 2006,  galGal3  recip best net
  - lamprey         Petromyzon marinus      June 2007, petMar1  recip best net

Files in this directory are:
    5way.mod      phastCons tree model with branch lengths for the 5 species
    chr*.data.gz - phastCons scores for the 5 species on chrM and chrUn

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/braFlo1/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

Checksum values for all files in this directory can be found in md5sum.txt.
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 - 5way.mod 2008-05-01 10:53 418 2008-05-01 13:34 14K 2008-05-01 13:37 37M md5sum.txt 2008-05-02 09:04 138