This directory contains compressed phastCons scores for multiple
alignments of 5 other vertebrate genomes to the lancelet genome:
- lancelet Branchiostoma floridae Mar 2006, braFlo1 reference
- human Homo sapiens Mar 2006, hg18 recip best net
- mouse Mus musculus July 2007, mm9 recip best net
- chicken Gallus gallus May 2006, galGal3 recip best net
- lamprey Petromyzon marinus June 2007, petMar1 recip best net
Files in this directory are:
5way.mod phastCons tree model with branch lengths for the 5 species
chr*.data.gz - phastCons scores for the 5 species on chrM and chrUn
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/braFlo1/multiz5way/
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/braFlo1/phastCons5way
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.
Checksum values for all files in this directory can be found in md5sum.txt.
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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 -
5way.mod 2008-05-01 10:53 418
chrM.data.gz 2008-05-01 13:34 14K
chrUn.data.gz 2008-05-01 13:37 37M
md5sum.txt 2008-05-02 09:04 138