This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/phyloP7way/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 6 vertebrate genomes to the medium ground finch genome,
plus two alternate sets of scores for subsets of species in the alignments.

Files in this directory are:

    geoFor1.phyloP.7way.mod - phyloP tree model with branch lengths for
                            all 7 species
    geoFor1.phyloP.birds.mod - tree model for the birds subset:
          geoFor1 taeGut1 melUnd1 galGal4 melGal1
          (medium ground finch, zebra finch, budgerigar, chicken, turkey)
    geoFor1.phyloP.vertebrate.mod - tree model for the vertebrate subset:
          geoFor1 hg19 mm10
          (medium ground finch, human, mouse)

Note, geoFor1 is included in each subset since it is the reference species.

PhyloP scores in bigWig format files:
    geoFor1.7way.phyloP7way.bw
    geoFor1.7way.phyloP7wayBirds.bw
    geoFor1.7way.phyloP7wayVertebrate.bw

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

PhyloP scores in fixed step wiggle format:
    geoFor1.7way.phyloP7way/phyloP7way.wigFix.gz - scores for all 7 species
    birds/phyloP7way.birds.wigFix.gz - scores for the birds subset
    vertebrate/phyloP7way.vertebrate.wigFix.gz - scores for the vertebrate subset

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/geoFor1/phastCons7way/

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/multiz7way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=geoFor1&g=cons7way

Assemblies used in these alignments:

==== reference assembly:
Medium ground finch - Geospiza fortis Apr. 2012  BGI/geoFor1       reference

==== Birds subset:
Zebra finch Taeniopygia guttata     Jul. 2008  WUGSC 3.2.4/taeGut1 Syntenic net
Budgerigar  Melopsittacus undulatus Sep. 2011  WUSTL v6.3/melUnd1  Syntenic net
Chicken  Gallus gallus              Nov. 2011  ICGSC 4.0/galGal4   Syntenic net
Turkey   Meleagris gallopavo        Dec. 2009  TGC 2.01/melGal1    Syntenic net

==== Vertebrate subset:
Human   Homo sapiens                Feb. 2009  GRCh37/hg19     Reciprocal best
Mouse   Mus musculus                Dec. 2019  GRCm38/mm10     Reciprocal best

---------------------------------------------------------------
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/geoFor1/phyloP7way/ ./

      OR

    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/geoFor1/phyloP7way

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)

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[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt07-Aug-2012 09:58 4.3K 
[DIR]birds/07-Aug-2012 09:45 -  
[SND]geoFor1.7way.phyloP.birds.mod06-Aug-2012 08:48 431  
[SND]geoFor1.7way.phyloP.vertebrate.mod03-Aug-2012 15:22 363  
[   ]geoFor1.7way.phyloP7way.bw03-Aug-2012 15:45 2.0G 
[SND]geoFor1.7way.phyloP7way.mod03-Aug-2012 14:24 480  
[DIR]geoFor1.7way.phyloP7way/07-Aug-2012 09:51 -  
[   ]geoFor1.7way.phyloP7wayBirds.bw06-Aug-2012 09:37 1.9G 
[   ]geoFor1.7way.phyloP7wayVertebrate.bw06-Aug-2012 08:52 578M 
[TXT]md5sum.txt07-Aug-2012 10:01 393  
[DIR]vertebrate/07-Aug-2012 09:47 -  

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