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

  - lamprey         Petromyzon marinus      June 2007, petMar1  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
  - medaka          Oryzias latipes         Apr 2006,  oryLat1  recip best net
  - Lancelet        Branchiostoma floridae  Mar 2006,  braFlo1  recip best net

Files in this directory are:
    6way.mod      phastCons tree model with branch lengths for the 6 species
    file_*.data.gz - phastCons scores for the 6 species
	each file contains the data for a number of contigs for Lamprey

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/petMar1/multiz6way/

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

---------------------------------------------------------------
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: 
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/petMar1/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 http://genome.ucsc.edu/goldenPath/credits.html.

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).
(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).
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[SND]6way.mod29-Apr-2008 09:05 426  
[TXT]README.txt21-May-2008 16:56 2.7K 
[   ]file_0.data.gz29-Apr-2008 11:42 3.8M 
[   ]file_1.data.gz29-Apr-2008 11:42 2.3M 
[   ]file_2.data.gz29-Apr-2008 11:42 1.7M 
[   ]file_3.data.gz29-Apr-2008 11:42 1.5M 
[   ]file_4.data.gz29-Apr-2008 11:42 1.2M 
[   ]file_5.data.gz29-Apr-2008 11:42 1.1M 
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[   ]file_63.data.gz29-Apr-2008 11:43 4.3K 
[TXT]md5sum.txt01-May-2008 16:15 3.2K 

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