This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/phastCons7way/README.txt

This directory contains compressed phastCons scores for multiple alignments
of 6 vertebrate genomes to the lizard genome.

Files in this directory are:
    vertebrate.mod      phastCons tree model with branch lengths
                        for all 7 species
		anoCar2 galGal3 gasAcu1 hg19 mm9 ornAna1 xenTro2
	  (lizard, chicken, stickleback, human, mouse, platypus, X. tropicalis)

    phastCons7way.wigFix.gz phastCons scores for 7 species, wiggle fixed step
    phastCons7way.bw phastCons scores for 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.cse.ucsc.edu/goldenPath/anoCar2/multiz7way/

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

Assemblies used in these alignments:

  - Lizard         Anolis carolinensis        May  2010  anoCar2/Broad
  - Chicken        Gallus gallus              May  2006  galGal3/WUGSC 2.1
  - Platypus       Ornithorhynchus anatinus   Mar. 2007  ornAna1/WUGSC 5.0.1
  - Human          Homo sapiens               Feb. 2009  hg19/GRCh37   
  - Mouse          Mus musculus               July 2007  mm9/NCBI37
  - X. tropicalis  Xenopus tropicalis         Aug. 2005  xenTro2/JGI 4.1
  - Stickleback    Gasterosteus aculeatus     Feb. 2006  gasAcu1/Broad

---------------------------------------------------------------
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.
There is approximately 8.5 Gb of compressed data in this directory.

Via rsync:
rsync -av --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/phastCons7way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/anoCar2/phastCons7way

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, 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)