This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/ce10/phyloP7way/README.txt

This directory contains conservation scoring by phyloP (phylogenetic p-values)
from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple
alignments of 6 Caenorhabditis nematode genomes to the C. elegans genome.

Files in this directory are:
    nematode.mod  phyloP tree model with branch lengths
                  for all 7 nematode species
	    ce10 caeSp91 caeRem4 caePb3 caeSp71 cb4 caeSp111 caeJap4 caeAng1
	(elegans, remanei, brenneri, briggsae, sp. 11, japonica, angaria)

    ce10.phyloP7way.wigFix.gz phyloP scores for all 7 species
    ce10.phyloP7way.bw phyloP scores for all 7 species in bigWig format

    md5sum.txt - md5 check sums of these files to verify correct download files

The multiple alignments and methods description are at:
http://hgdownload.test.cse.ucsc.edu/goldenPath/ce10/multiz7way/

PhastCons conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/ce10/phastCons7way

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=ce10&g=cons7way

Assemblies used in these alignments:

  - C. elegans                       Oct. 2010  ce10/WS220
  - C. briggsae                      Apr. 2011  cb4/WS225
  - C. remanei                       July 2007  caeRem4/WS220
  - C. sp. 11 ju1373                 Nov. 2010  caeSp111/GCA_000186765.1
  - C. brenneri                      Nov. 2010  caePb3/GCA_000143925.1
  - C. japonica                      Aug. 2010  caeJap4/GCA_000147155.1
  - C. angaria                       Oct. 2010  caeAng1/GCA_000165025.1/WS225

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To download a large file or multiple files from this directory, we recommend 
that you use rsync or ftp rather than downloading the files via our website:

   rsync -av --progress \
        rsync://hgdownload.cse.ucsc.edu/goldenPath/ce10/phyloP7way/ ./

      OR

    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/ce10/phyloP7way

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.

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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.

---------------------------------------------------------------
References for phastCons and phyloP:

Pollard KS, Hubisz MJ, Siepel A. Detection of non-neutral substitution rates
on mammalian phylogenies. Genome Res. 2009 Oct 26. [Epub ahead of print]
(http://genome.cshlp.org/content/early/2009/10/26/gr.097857.109.abstract)

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson
H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements
in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005
Aug;15(8):1034-50.  (http://www.genome.org/cgi/doi/10.1101/gr.3715005)