This directory contains compressed phastCons scores for multiple
alignments of 8 other vertebrate genomes to the marmoset genome:
- marmoset Callithrix jacchus June 2007, calJac1 reference
- human Homo sapiens Mar 2006, hg18 recip best net
- chimpanzee Pan troglodytes Mar 2006, panTro2 recip best net
- orangutan Pongo pygmaeus abelii July 2007, ponAbe2 recip best net
- rhesus Macaca mulatta Jan 2006, rheMac2 recip best net
- mouse Mus musculus July 2007, mm9 recip best net
- dog Canis familiaris May 2005, canFam2 recip best net
- opossum Monodelphis domestica Jan 2006, monDom4 chain net
- platypus Ornithorhychus anatinus Mar 2007, ornAna1 chain net
Files in this directory are:
9way.mod phastCons tree model with branch lengths for the 9 species
file_*.data.gz - phastCons scores for the 9 species
each file contains the data for a number of contigs for Marmoset
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/calJac1/multiz9way/
For a description of the phastCons file format, see
http://genome.ucsc.edu/goldenPath/help/phastCons.html.
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To download a large file or multiple files from this directory, we recommend
that you use ftp rather than downloading the files via our website. To do so:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/calJac1/phastCons9way
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.
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References for phastCons:
Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A., Hou, M.,
Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S.,
Weinstock, G.M., Wilson, R. K., Gibbs, R.A., Kent, W.J., Miller, W.,
and Haussler, D. Evolutionarily conserved elements in vertebrate, insect,
worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).
(http://www.genome.org/cgi/doi/10.1101/gr.3715005)
Siepel, A. and Haussler, D. Phylogenetic hidden Markov models.
In R. Nielsen, ed., Statistical Methods in Molecular Evolution,
Springer (in press) (2004).
Name Last modified Size Description
Parent Directory -
9way.mod 2008-01-09 15:35 530
file_0.data.gz 2008-01-10 14:43 1.1G
file_1.data.gz 2008-01-10 14:50 543M
file_2.data.gz 2008-01-10 14:54 361M
file_3.data.gz 2008-01-10 14:57 251M
file_4.data.gz 2008-01-10 14:59 180M
file_5.data.gz 2008-01-10 15:01 124M
file_6.data.gz 2008-01-10 15:03 86M
file_7.data.gz 2008-01-10 15:03 57M
file_8.data.gz 2008-01-10 15:04 35M
file_9.data.gz 2008-01-10 15:04 23M
file_10.data.gz 2008-01-10 15:05 16M
file_11.data.gz 2008-01-10 15:05 12M
file_12.data.gz 2008-01-10 15:05 9.7M
file_13.data.gz 2008-01-10 15:06 7.4M
file_14.data.gz 2008-01-10 15:06 6.2M
file_15.data.gz 2008-01-10 15:06 5.3M
file_16.data.gz 2008-01-10 15:06 4.1M
file_17.data.gz 2008-01-10 15:06 2.7M
file_18.data.gz 2008-01-10 15:06 2.0M
file_19.data.gz 2008-01-10 15:07 1.7M
file_20.data.gz 2008-01-10 15:07 1.3M
file_21.data.gz 2008-01-10 15:07 1.0M
file_22.data.gz 2008-01-10 15:07 933K
file_23.data.gz 2008-01-10 15:07 699K
file_24.data.gz 2008-01-10 15:07 601K
file_25.data.gz 2008-01-10 15:07 718K
file_26.data.gz 2008-01-10 15:07 766K
file_27.data.gz 2008-01-10 15:07 713K
file_28.data.gz 2008-01-10 15:07 595K
file_29.data.gz 2008-01-10 15:07 545K
file_30.data.gz 2008-01-10 15:07 579K
file_31.data.gz 2008-01-10 15:07 544K
file_32.data.gz 2008-01-10 15:07 3.7K
md5sum.txt 2008-04-22 11:01 1.6K