This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/mm9/phyloP30way/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 29 vertebrate genomes to the mouse genome, plus alternate sets
of scores for the euarchontoglire species and the placental mammal species in the
alignments.

Files in this directory are:
    vertebrate.mod      phyloP tree model with branch lengths
                        for all 30 species.
    euarchontoglires.mod  phyloP tree model for the euarchontoglires subset:
	mm9, rn4, cavPor2, oryCun1, hg18, panTro2, ponAbe2, rheMac2, calJac1,
	otoGar1, tupBel1
	(mouse, rat, guinea pig, rabbit, human, chimp, orangutan, rhesus,
	marmoset, bushbaby, tree shrew)
    placentalMammals.mod   phyloP tree model for the placental mammal subset:
	mm9, rn4, cavPor2, oryCun1, hg18, panTro2, ponAbe2, rheMac2, calJac1,
	otoGar1, tupBel1, sorAra1, eriEur1, canFam2, felCat3, equCab1, bosTau3,
	dasNov1, loxAfr1, echTel1
	(mouse, rat, guinea pig, rabbit, human, chimp, orangutan, rhesus,
	marmoset, bushbaby, tree shrew, shrew, hedgehog, dog, cat,
	horse, cow, armadillo, elephant, tenrec)

    vertebrate/*.wigFix.gz phyloP scores for all 30 species
    euarchontoglires/*.wigFix.gz  phyloP scores for euarchontoglire subset
    placentalMammals/*.wigFix.gz  phyloP scores for placental mammal subset

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/mm9/multiz30way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=cons30way

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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 -avz --progress \
        rsync://hgdownload.cse.ucsc.edu/goldenPath/mm9/phyloP30way/ ./

      OR

    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/mm9/phyloP30way

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.

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

Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral
substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21.
Epub 2009 Oct 26.  (http://genome.cshlp.org/content/20/1/110.long)

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)