This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/calJac3/phastCons13way/README.txt


This directory contains compressed phastCons scores for multiple alignments
of 12 vertebrate genomes to the marmoset genome:


  - marmoset        Callithrix jacchus      Mar 2009, calJac3  reference
  - human           Homo sapiens            Feb 2009, hg19     chain nboon
  - Chimp           Pan troglodytes         Mar 2006, panTro2  chain net
  - Gorilla         Gorilla gorilla gorilla Oct 2009, gorGor2  recip best
  - Orangutan       Pongo pygmaeus abelii   July 2007, ponAbe2 chain net
  - Baboon          Papio hamadryas         Nov 2008, papHam1  recip best
  - Rhesus          Macaca mulatta          Jan 2006,  rheMac2 chain net
  - Tarsier         Tarsier syrichta        Aug 2008,  tarSyr1 recip best
  - Mouse lemur     Microcebus murinus      Jun 2003,  micMur1 recip best
  - Bushbaby        Otolemur garnettii      Dec 2006, otoGar1  recip best
  - Mouse           Mus musculus            July 2007, mm9     chain net
  - Dog             Canis lupus familiaris  May 2005, canFam2  chain net
  - Opossum         Monodelphis domestica   Oct 2006,  monDom5 chain net
  
  
  

Files in this directory are:
    all.mod      phastCons tree model with branch lengths
                 for all 13 species

    phastCons13way.wigFix.gz phastCons scores for 13 species

    histo.png    histogram of phastCons scores

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/calJac3/multiz13way/

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

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=calJac3&g=cons13way

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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.
There is approximately 333 MB of compressed data in this directory.

Via rsync:
rsync -avz --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/calJac3/phastCons13way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/calJac3/phastCons13way

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)