This directory contains compressed phastCons scores for multiple
alignments of 8 other vertebrate genomes to the marmoset genome:

  - marmoset        Callithrix jacchus      June 2007, calJac1  reference
  - human           Homo sapiens            Mar 2006, hg18      recip best net
  - chimpanzee      Pan troglodytes         Mar 2006, panTro2   recip best net
  - orangutan       Pongo pygmaeus abelii   July 2007, ponAbe2  recip best net
  - rhesus          Macaca mulatta          Jan 2006, rheMac2   recip best net
  - mouse           Mus musculus            July 2007, mm9      recip best net
  - dog             Canis familiaris        May 2005, canFam2   recip best net
  - opossum         Monodelphis domestica   Jan 2006, monDom4   chain net
  - platypus        Ornithorhychus anatinus Mar 2007, ornAna1   chain net

Files in this directory are:
    9way.mod      phastCons tree model with branch lengths for the 9 species
    file_*.data.gz - phastCons scores for the 9 species
	each file contains the data for a number of contigs for Marmoset

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/calJac1/multiz9way/

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/calJac1/phastCons9way

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:

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]9way.mod09-Jan-2008 15:35 530  
[TXT]README.txt28-Mar-2008 15:57 2.8K 
[   ]file_0.data.gz10-Jan-2008 14:43 1.1G 
[   ]file_1.data.gz10-Jan-2008 14:50 543M 
[   ]file_2.data.gz10-Jan-2008 14:54 361M 
[   ]file_3.data.gz10-Jan-2008 14:57 251M 
[   ]file_4.data.gz10-Jan-2008 14:59 180M 
[   ]file_5.data.gz10-Jan-2008 15:01 124M 
[   ]file_6.data.gz10-Jan-2008 15:03 86M 
[   ]file_7.data.gz10-Jan-2008 15:03 57M 
[   ]file_8.data.gz10-Jan-2008 15:04 35M 
[   ]file_9.data.gz10-Jan-2008 15:04 23M 
[   ]file_10.data.gz10-Jan-2008 15:05 16M 
[   ]file_11.data.gz10-Jan-2008 15:05 12M 
[   ]file_12.data.gz10-Jan-2008 15:05 9.7M 
[   ]file_13.data.gz10-Jan-2008 15:06 7.4M 
[   ]file_14.data.gz10-Jan-2008 15:06 6.2M 
[   ]file_15.data.gz10-Jan-2008 15:06 5.3M 
[   ]file_16.data.gz10-Jan-2008 15:06 4.1M 
[   ]file_17.data.gz10-Jan-2008 15:06 2.7M 
[   ]file_18.data.gz10-Jan-2008 15:06 2.0M 
[   ]file_19.data.gz10-Jan-2008 15:07 1.7M 
[   ]file_20.data.gz10-Jan-2008 15:07 1.3M 
[   ]file_21.data.gz10-Jan-2008 15:07 1.0M 
[   ]file_22.data.gz10-Jan-2008 15:07 933K 
[   ]file_23.data.gz10-Jan-2008 15:07 699K 
[   ]file_24.data.gz10-Jan-2008 15:07 601K 
[   ]file_25.data.gz10-Jan-2008 15:07 718K 
[   ]file_26.data.gz10-Jan-2008 15:07 766K 
[   ]file_27.data.gz10-Jan-2008 15:07 713K 
[   ]file_28.data.gz10-Jan-2008 15:07 595K 
[   ]file_29.data.gz10-Jan-2008 15:07 545K 
[   ]file_30.data.gz10-Jan-2008 15:07 579K 
[   ]file_31.data.gz10-Jan-2008 15:07 544K 
[   ]file_32.data.gz10-Jan-2008 15:07 3.7K 
[TXT]md5sum.txt22-Apr-2008 11:01 1.6K 

Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80