This directory contains compressed phastCons scores for multiple
alignments of the following assemblies to the D. melanogaster genome
(dm3, Apr. 2006, BDGP Release 5).

- D. simulans (droSim1, Apr. 2005)
- D. sechellia (droSec1, Oct. 2005)
- D. yakuba (droYak2, Nov. 2005)
- D. erecta (droEre2, Feb. 2006)
- D. ananassae (droAna3, Feb. 2006)
- D. pseudoobscura (dp4, Feb. 2006) 
- D. persimilis (droPer1, Oct. 2005)
- D. willistoni (droWil1, Feb. 2006)
- D. virilis (droVir3, Feb. 2006) 
- D. mojavensis (droMoj3, Feb. 2006) 
- D. grimshawi (droGri2, Feb. 2006)
- A. gambiae (anoGam1, Feb. 2003) 
- A. mellifera (apiMel3, May 2005) 
- T. castaneum (triCas2, Sep. 2005)

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

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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/dm3/phastCons15way

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. and Haussler, D. Phylogenetic hidden Markov models.
In R. Nielsen, ed., Statistical Methods in Molecular Evolution,
Springer (in press) (2004).

A manuscript on phastCons is in preparation.

For a discussion of the methods used to calculate the phastCons scores,
see the description page for the Conservation track in the Genome
Browser.

      Name                    Last modified      Size  Description
      Parent Directory                             -   
      ave.cons.mod            2007-02-06 09:27  697   
      ave.noncons.mod         2007-02-06 09:27  697   
      md5sum.txt              2006-12-11 17:48  706   
      chrM.pp.gz              2006-12-11 17:48   24K  
      chrXHet.pp.gz           2006-12-11 17:48  230K  
      chrYHet.pp.gz           2006-12-11 17:48  284K  
      chr2LHet.pp.gz          2006-12-11 17:46  325K  
      chr4.pp.gz              2006-12-11 17:47  1.5M  
      chr3RHet.pp.gz          2006-12-11 17:47  2.5M  
      chr3LHet.pp.gz          2006-12-11 17:46  2.6M  
      chr2RHet.pp.gz          2006-12-11 17:46  3.0M  
      chrU.pp.gz              2006-12-11 17:47  8.4M  
      chrUextra.pp.gz         2006-12-11 17:47   25M  
      chr2R.pp.gz             2006-12-11 17:46   28M  
      chr2L.pp.gz             2006-12-11 17:46   30M  
      chrX.pp.gz              2006-12-11 17:48   30M  
      chr3L.pp.gz             2006-12-11 17:46   32M  
      chr3R.pp.gz             2006-12-11 17:47   37M