This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/calJac3/phastCons13way/README.txt
This directory contains compressed phastCons scores for multiple alignments
of 12 vertebrate genomes to the marmoset genome:
- marmoset Callithrix jacchus Mar 2009, calJac3 reference
- human Homo sapiens Feb 2009, hg19 chain nboon
- Chimp Pan troglodytes Mar 2006, panTro2 chain net
- Gorilla Gorilla gorilla gorilla Oct 2009, gorGor2 recip best
- Orangutan Pongo pygmaeus abelii July 2007, ponAbe2 chain net
- Baboon Papio hamadryas Nov 2008, papHam1 recip best
- Rhesus Macaca mulatta Jan 2006, rheMac2 chain net
- Mouse lemur Microcebus murinus Jun 2003, micMur1 recip best
- Tarsier Tarsier syrichta Aug 2008, tarSyr1 recip best
- Bushbaby Otolemur garnettii Dec 2006, otoGar1 recip best
- Mouse Mus musculus July 2007, mm9 chain net
- Dog Canis lupus familiaris May 2005, canFam2 chain net
- Opossum Monodelphis domestica Oct 2006, monDom5 chain net
Files in this directory are:
all.mod phastCons tree model with branch lengths
for all 13 species
phastCons13way.wigFix.gz phastCons scores for 13 species
histo.png histogram of phastCons scores
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/calJac3/multiz13way/
For a description of the phastCons data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
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.
There is approximately 333 MB of compressed data in this directory.
Via rsync:
rsync -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/calJac3/phastCons13way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/calJac3/phastCons13way
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.
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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 -
md5sum.txt 2011-05-02 11:05 190
all.mod 2011-04-27 16:25 696
histo.png 2011-04-29 11:20 6.1K
phastCons13way.wigFix.gz 2011-04-28 16:34 2.5G