This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/xenTro9/phyloP11way/README.txt

This directory contains conservation scoring by phyloP (phylogenetic p-values)
from the PHAST package (http://compgen.cshl.edu/phast/) for multiple
alignments of 10 genome sequences to the X. tropicalis genome.

Files in this directory:

    xenTro9.phyloP11way.wigFix.gz - scores in fixed step wiggle format
    xenTro9.phyloP11way.mod - phyloP tree model with branch lengths for
                            all 11 species
    xenTro9.phyloP11way.bw - scores in bigWig format
    md5sum.txt - MD5 checksums to verify download files

See also: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
   for bigWig format description

For a description of the fixed step wiggle data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html

The phastCons data can be found at:
http://hgdownload.cse.ucsc.edu/goldenPath/xenTro9/phastCons11way/

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/xenTro9/multiz11way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=xenTro9&g=cons11way

-----------------------------------------------------------------------------
Assemblies used in these alignments:

- X. tropicalis       Xenopus tropicalis     Jul. 2016  DOE JGI v9.1/xenTro9
                                                        reference genome

- African clawed frog Xenopus laevis         Aug. 2016  IXSC v2/xenLae2
- Tibetan frog        Nanorana parkeri       Mar. 2015  BGI ZX_2015/nanPar1
- Painted turtle      Chrysemys picta bellii Mar. 2014  IPTGSC v3.0.3/chrPic2
- Chicken             Gallus gallus          May  2006  Gallus_gallus-5.0/galGal5
- Lizard              Anolis carolinensis    May  2010  anoCar2/Broad
- Opossum             Monodelphis domestica  Oct. 2006  Broad/monDom5
- Dog                 Canis lupus familiaris Sep. 2011  Broad CanFam3.1/canFam3
- Human               Homo sapiens           Dec. 2013  GRCh38/hg38
- Mouse               Mus musculus           Dec. 2011  GRCm38/mm10
- Fugu                Takifugu rubripes      Oct. 2011  FUGU5/fr3

Syntenic net filtered MAF files used for multiz:
   hg38, mm10, xenLae2, canFam3, monDom5, fr3, galGal5, anoCar2
Reciprocal best filtered MAF files used for multiz:
   nanPar1 chrPic2

-----------------------------------------------------------------------------
Note, the uncompressed *wigFix.gz file is 2.8 Gb of data, when compressed, 
it is approximately 408 Mb of compressed data.  The entire set of
data in this directory is approximately 1.3 Gb.

To download a large file or multiple files from this directory, we recommend 
that you use rsync or ftp rather than downloading the files via our website:

   rsync -avz --progress \
        rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro9/phyloP11way/ ./

      OR

    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/xenTro9/phyloP11way

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 and phyloP:

Pollard KS, Hubisz MJ, Siepel A. Detection of non-neutral substitution rates
on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21.
(http://genome.cshlp.org/content/20/1/110.long)

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson
H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements
in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005
Aug;15(8):1034-50.  (http://genome.cshlp.org/content/15/8/1034.full)

---------------------------------------------------------------