This directory contains compressed phastCons scores for multiple
alignments of the following assemblies to the D. melanogaster genome
(dm2, Apr. 2004, BDGP Release 4 + DHGP Release 3.2).  

- D. simulans (droSim1, Apr. 2005)
- D. yakuba (droYak1, Apr. 2004)
- D. ananassae (droAna1, Jul. 2004)
- D. pseudoobscura (dp3, Nov. 2004)
- D. virilis (droVir1, Jul. 2004) 
- D. mojavensis (droMoj1, Aug. 2004) 
- A. gambiae (anoGam1, Feb. 2003) 
- A. mellifera (apiMel1, Jul. 2004) 

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

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If you plan to download a large file or multiple files from this 
directory, we recommend you use ftp rather than downloading the files 
via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to 
the directory goldenPath/dm2/phastCons9way. To download multiple files, 
use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory)

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 .

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References for phastCons:

Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, 
worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).

Siepel, A. and Haussler, D. Phylogenetic hidden Markov models. In Statistical
Methods in Molecular Evolution (ed. Nielsen, R.) (Springer, 2005). 

For a discussion of the methods used to calculate the phastCons scores,
see the description page for the dm2 Conservation track in the Genome
Browser.

      Name                    Last modified      Size  Description
      Parent Directory                             -   
      md5sum.txt              2005-05-27 18:16  594   
      chrYh.pp.gz             2005-05-27 18:16  236K  
      chrXh.pp.gz             2005-05-27 18:16  419K  
      chrX.pp.gz              2005-05-27 18:15   31M  
      chrU.pp.gz              2005-05-27 18:14  3.7M  
      chrM.pp.gz              2005-05-27 18:14   24K  
      chr4h.pp.gz             2005-05-27 18:16   77K  
      chr4.pp.gz              2005-05-27 18:14  1.6M  
      chr3h.pp.gz             2005-05-27 18:16  2.0M  
      chr3R.pp.gz             2005-05-27 18:16   38M  
      chr3L.pp.gz             2005-05-27 18:16   32M  
      chr2h.pp.gz             2005-05-27 18:15  1.3M  
      chr2R.pp.gz             2005-05-27 18:15   28M  
      chr2L.pp.gz             2005-05-27 18:15   30M