This directory contains compressed phastCons scores for multiple
alignments of 5 other vertebrate genomes to the lamprey genome:
- lamprey Petromyzon marinus June 2007, petMar1 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
- medaka Oryzias latipes Apr 2006, oryLat1 recip best net
- Lancelet Branchiostoma floridae Mar 2006, braFlo1 recip best net
Files in this directory are:
6way.mod phastCons tree model with branch lengths for the 6 species
file_*.data.gz - phastCons scores for the 6 species
each file contains the data for a number of contigs for Lamprey
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/petMar1/multiz6way/
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/petMar1/phastCons6way
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 -
6way.mod 2008-04-29 09:05 426
md5sum.txt 2008-05-01 16:15 3.2K
file_61.data.gz 2008-04-29 11:43 3.4K
file_63.data.gz 2008-04-29 11:43 4.3K
file_62.data.gz 2008-04-29 11:43 6.9K
file_54.data.gz 2008-04-29 11:43 12K
file_53.data.gz 2008-04-29 11:43 15K
file_60.data.gz 2008-04-29 11:43 16K
file_50.data.gz 2008-04-29 11:43 18K
file_59.data.gz 2008-04-29 11:43 19K
file_51.data.gz 2008-04-29 11:43 20K
file_55.data.gz 2008-04-29 11:43 21K
file_58.data.gz 2008-04-29 11:43 21K
file_52.data.gz 2008-04-29 11:43 25K
file_49.data.gz 2008-04-29 11:43 26K
file_56.data.gz 2008-04-29 11:43 27K
file_44.data.gz 2008-04-29 11:43 30K
file_41.data.gz 2008-04-29 11:43 34K
file_48.data.gz 2008-04-29 11:43 35K
file_45.data.gz 2008-04-29 11:43 35K
file_47.data.gz 2008-04-29 11:43 35K
file_46.data.gz 2008-04-29 11:43 38K
file_43.data.gz 2008-04-29 11:43 39K
file_40.data.gz 2008-04-29 11:43 40K
file_42.data.gz 2008-04-29 11:43 46K
file_39.data.gz 2008-04-29 11:43 47K
file_36.data.gz 2008-04-29 11:43 48K
file_57.data.gz 2008-04-29 11:43 58K
file_37.data.gz 2008-04-29 11:43 60K
file_38.data.gz 2008-04-29 11:43 60K
file_34.data.gz 2008-04-29 11:43 69K
file_35.data.gz 2008-04-29 11:43 81K
file_33.data.gz 2008-04-29 11:43 95K
file_32.data.gz 2008-04-29 11:43 125K
file_29.data.gz 2008-04-29 11:43 145K
file_31.data.gz 2008-04-29 11:43 161K
file_28.data.gz 2008-04-29 11:43 177K
file_27.data.gz 2008-04-29 11:43 180K
file_25.data.gz 2008-04-29 11:43 189K
file_23.data.gz 2008-04-29 11:43 199K
file_26.data.gz 2008-04-29 11:43 208K
file_30.data.gz 2008-04-29 11:43 209K
file_24.data.gz 2008-04-29 11:43 244K
file_22.data.gz 2008-04-29 11:43 288K
file_19.data.gz 2008-04-29 11:43 326K
file_21.data.gz 2008-04-29 11:43 344K
file_20.data.gz 2008-04-29 11:43 370K
file_17.data.gz 2008-04-29 11:43 407K
file_16.data.gz 2008-04-29 11:43 416K
file_18.data.gz 2008-04-29 11:43 424K
file_15.data.gz 2008-04-29 11:43 464K
file_14.data.gz 2008-04-29 11:43 498K
file_13.data.gz 2008-04-29 11:43 528K
file_12.data.gz 2008-04-29 11:43 642K
file_11.data.gz 2008-04-29 11:43 654K
file_10.data.gz 2008-04-29 11:43 667K
file_8.data.gz 2008-04-29 11:43 746K
file_9.data.gz 2008-04-29 11:43 801K
file_7.data.gz 2008-04-29 11:42 942K
file_6.data.gz 2008-04-29 11:42 1.0M
file_5.data.gz 2008-04-29 11:42 1.1M
file_4.data.gz 2008-04-29 11:42 1.2M
file_3.data.gz 2008-04-29 11:42 1.5M
file_2.data.gz 2008-04-29 11:42 1.7M
file_1.data.gz 2008-04-29 11:42 2.3M
file_0.data.gz 2008-04-29 11:42 3.8M