This directory contains compressed phastCons scores for multiple
alignments of 30 vertebrate genomes to the mouse genome,
plus an alternate set of scores for the euchontoglires
subset of species in the alignments,
and an alternate set of scores for the placental mammal
subset of species in the alignments.
Files in this directory are:
vertebrate.mod phastCons tree model with branch lengths
for all 30 species
euarchontoglires.mod phastCons tree model for the euarchontoglires subset
placental.mod phastCons tree model for the placental subset
vertebrate/*.data.gz phastCons scores for 30 species
euarchontoglires/*.data.gz phastCons scores for placental subset (11 species)
placental/*.data.gz phastCons scores for placental subset (20 species)
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/mm9/multiz30way/
For a description of the phastCons file format, see
http://genome.ucsc.edu/goldenPath/help/phastCons.html.
---------------------------------------------------------------
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/mm9/phastCons30way
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:
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 -
euarchontoglires.mod 2007-10-31 10:30 582
euarchontoglires/ 2007-11-05 10:45 -
placental.mod 2007-10-31 12:33 834
placental/ 2007-11-05 10:44 -
vertebrate.mod 2007-10-22 16:42 1.1K
vertebrate/ 2007-11-05 10:44 -