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 - md5sum.txt 2008-05-01 16:15 3.2K file_63.data.gz 2008-04-29 11:43 4.3K file_62.data.gz 2008-04-29 11:43 6.9K file_61.data.gz 2008-04-29 11:43 3.4K file_60.data.gz 2008-04-29 11:43 16K file_59.data.gz 2008-04-29 11:43 19K file_58.data.gz 2008-04-29 11:43 21K file_57.data.gz 2008-04-29 11:43 58K file_56.data.gz 2008-04-29 11:43 27K file_55.data.gz 2008-04-29 11:43 21K file_54.data.gz 2008-04-29 11:43 12K file_53.data.gz 2008-04-29 11:43 15K file_52.data.gz 2008-04-29 11:43 25K file_51.data.gz 2008-04-29 11:43 20K file_50.data.gz 2008-04-29 11:43 18K file_49.data.gz 2008-04-29 11:43 26K file_48.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_45.data.gz 2008-04-29 11:43 35K file_44.data.gz 2008-04-29 11:43 30K file_43.data.gz 2008-04-29 11:43 39K file_42.data.gz 2008-04-29 11:43 46K file_41.data.gz 2008-04-29 11:43 34K file_40.data.gz 2008-04-29 11:43 40K file_39.data.gz 2008-04-29 11:43 47K file_38.data.gz 2008-04-29 11:43 60K file_37.data.gz 2008-04-29 11:43 60K file_36.data.gz 2008-04-29 11:43 48K file_35.data.gz 2008-04-29 11:43 81K file_34.data.gz 2008-04-29 11:43 69K file_33.data.gz 2008-04-29 11:43 95K file_32.data.gz 2008-04-29 11:43 125K file_31.data.gz 2008-04-29 11:43 161K file_30.data.gz 2008-04-29 11:43 209K file_29.data.gz 2008-04-29 11:43 145K file_28.data.gz 2008-04-29 11:43 177K file_27.data.gz 2008-04-29 11:43 180K file_26.data.gz 2008-04-29 11:43 208K file_25.data.gz 2008-04-29 11:43 189K file_24.data.gz 2008-04-29 11:43 244K file_23.data.gz 2008-04-29 11:43 199K file_22.data.gz 2008-04-29 11:43 288K file_21.data.gz 2008-04-29 11:43 344K file_20.data.gz 2008-04-29 11:43 370K file_19.data.gz 2008-04-29 11:43 326K file_18.data.gz 2008-04-29 11:43 424K file_17.data.gz 2008-04-29 11:43 407K file_16.data.gz 2008-04-29 11:43 416K 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_9.data.gz 2008-04-29 11:43 801K file_8.data.gz 2008-04-29 11:43 746K 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 6way.mod 2008-04-29 09:05 426