This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/dm6/phyloP27way/README.txt

This directory contains conservation scoring by phyloP (phylogenetic p-values)
from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple
alignments of 26 genomes to the D. melanogaster genome.

Files in this directory:

    dm6.phyloP27way.mod - phyloP tree model with branch lengths for
                            all 27 species
    dm6.phyloP27way.bw  - scores in bigWig format
    dm6.phyloP27way.wigFix.gz - scores in fixed step wiggle format

See also: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
   for bigWig format description

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

The phastCons data can be found at:
http://hgdownload.cse.ucsc.edu/goldenPath/dm6/phastCons27way/

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/dm6/multiz27way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=dm6&g=cons27way

Assemblies used in these alignments:                                (alignment
                                                                         type)

D. melanogaster      Aug. 2014  (BDGP Release 6 + ISO1 MT/dm6)       reference
D. simulans          Apr. 2005  (WUGSC 1.0/droSim1)                  syntenic
D. sechellia         Oct. 2005  (Broad/droSec1)                      syntenic
D. yakuba            Jun. 2006  (Flybase dyak_caf1/droYak3)          syntenic
D. erecta            Feb. 2006  (Agencourt CAF1/droEre2)             syntenic
D. biarmipes         Mar. 2013  (BCM Dbia_2.0/droBia2)               syntenic
D. suzukii           Sep. 2013  (BGI Dsuzukii.v01/droSuz1)           syntenic
D. ananassae         Feb. 2006  (Agencourt CAF1/droAna3)             syntenic
D. bipectinata       Mar. 2013  (BCM Dbip_2.0/droBip2)               syntenic
D. eugracilis        Mar. 2013  (modENCODE Deug_2.0/droEug2)         syntenic
D. elegans           Mar. 2013  (BCM Dele_2.0/droEle2)               syntenic
D. kikkawai          Mar. 2013  (BCM Dkik_2.0/droKik2)               syntenic
D. takahashii        Mar. 2013  (BCM Dtak_2.0/droTak2)               syntenic
D. rhopaloa          Feb. 2013  (modENCODE Drho_2.0/droRho2)         syntenic
D. ficusphila        Mar. 2013  (BCM Dfic_2.0/droFic2)               syntenic
D. pseudoobscura     Apr. 2013  (BCM Dpse_3.0/droPse3)               syntenic
D. persimilis        Oct. 2005  (Broad/droPer1)                      syntenic
D. miranda           Apr. 2013  (U.C. Berkeley DroMir_2.2/droMir2)   syntenic
D. willistoni        Aug. 2006  (JCVI dwil_caf1/droWil2)             syntenic
D. virilis           Feb. 2006  (Agencourt CAF1/droVir3)             syntenic
D. mojavensis        Feb. 2006  (Agencourt CAF1/droMoj3)             syntenic
D. albomicans        May. 2012  (Kunming DroAlb_1.0/droAlb1)         syntenic
D. grimshawi         Feb. 2006  (Agencourt CAF1/droGri2)             syntenic
Musca domestica      Apr. 2013  (Glossina M_domestica-2.0.2/musDom2) net
Anopheles gambiae    Feb. 2003  (IAGEC MOZ2/anoGam1)                 net
Apis mellifera       Nov. 2010  (BCM Amel_4.5/apiMel4)               net
Tribolium castaneum  Sep. 2005  (BCM 2.0/triCas2)                    net

---------------------------------------------------------------
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:

   rsync -avz --progress \
        rsync://hgdownload.cse.ucsc.edu/goldenPath/dm6/phyloP27way/ ./

      OR

    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/dm6/phyloP227way

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. 2010 Jan;20(1):110-21.
(http://genome.cshlp.org/content/20/1/110.long)

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://genome.cshlp.org/content/15/8/1034.full)

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[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt21-Nov-2014 12:38 5.0K 
[   ]dm6.phyloP27way.bw05-Dec-2014 14:23 396M 
[SND]dm6.phyloP27way.mod13-Nov-2014 15:29 1.0K 
[   ]dm6.phyloP27way.wigFix.gz05-Dec-2014 14:19 225M 
[TXT]md5sum.txt05-Dec-2014 14:36 167  

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