This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/calJac3/phyloP13way/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 12 vertebrate genomes to the marmoset genome.
of scores for the primate species and the placental mammal species in the
alignments.
Files in this directory are:
all.mod phyloP tree model with branch lengths
for all 13 species:
marmoset (calJac3)
human (hg19)
Baboon (papHam1)
Bushbaby (otoGar1)
Chimp (panTro2)
Dog (canFam2)
Gorilla (gorGor2)
Mouse (mm9)
Opossum (monDom5)
Orangutan (ponAbe2)
Rhesus (rheMac2)
Mouse (micMur1)
Tarsier (tarSyr1)
vertebrate/*.wigFix.gz phyloP scores for all 13 species
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/calJac3/multiz13way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=calJac3&g=cons13way
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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/calJac3/phyloP13way/ ./
OR
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/calJac3/phyloP13way
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)
Name Last modified Size Description
Parent Directory -
vertebrate/ 2011-05-01 14:49 -
md5sum.txt 2011-05-02 11:22 87
all.mod 2011-04-29 15:42 665