This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/ce11/phastCons26way/README.txt

This directory contains compressed phastCons scores for multiple alignments
of 25 nematode genomes to the C. elegans genome.

Files in this directory are:
    ce11.phastCons26way.mod  phastCons tree model with branch lengths
                        for the 26 species
    ce11.phastCons26way.wigFix.gz - phastCons scores for the 26 species
                        in fixed step wiggle format
    ce11.phastCons26way.bw - phastCons scores for all 26 nematode species
                        in bigWig format
    md5sum.txt - md5 sums of the files here to verify accurate download

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/ce11/multiz26way/

For a description of the wigFix data file format, note the section
describing the 'fixedStep' wiggle format:
http://genome.ucsc.edu/goldenPath/help/wiggle.html

For a description of the phastCons data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
see also the section describing the 'fixedStep' wiggle format:
http://genome.ucsc.edu/goldenPath/help/wiggle.html

Assemblies used in these alignments:

C. elegans         Caenorhabditis elegans   Feb. 2013 (WBcel235/ce11) reference

A. ceylanicum      Ancylostoma ceylanicum   Mar. 2014
                                         (WS243/Acey_2013.11.30.genDNA/ancCey1)
Barber pole worm   Haemonchus contortus     Jul. 2013  (WormBase WS239/haeCon2)
C. angaria         Caenorhabditis angaria   Mar. 2012           (WS245/caeAng2)
C. brenneri        Caenorhabditis brenneri  Nov. 2010
                                                    (C. brenneri 6.0.1b/caePb3)
C. briggsae        Caenorhabditis briggsae  Apr. 2011               (WS225/cb4)
C. japonica        Caenorhabditis japonica  Aug. 2010     (WUSTL 7.0.1/caeJap4)
C. remanei         Caenorhabditis remanei   Jul. 2007           (WS220/caeRem4)
C. sp. 5 ju800     Caenorhabditis sp5 ju800 Jan. 2012
                                  (WS230/Caenorhabditis_sp_5-JU800-1.0/caeSp51)
C. tropicalis      Caenorhabditis tropicalis Nov. 2010   (WUSTL 3.0.1/caeSp111)
Dog heartworm      Dirofilaria immitis      Sep. 2013
                                                (WS240/D. immitis v2.2/dirImm1)
Eye worm           Loa loa                  Jul. 2012
                                         (WS235/L_loa_Cameroon_isolate/loaLoa1)
Filarial worm      Brugia malayi            May. 2014
                                                   (WS244/B_malayi-3.1/bruMal2)
H. bacteriophora/m31e Heterorhabditis bacteriophora Aug. 2011
                                           (WS229/H. bacteriophora 7.0/hetBac1)
M. hapla           Meloidogyne hapla        Sep. 2008
                                                   (M. hapla VW9 WS210/melHap1)
M. incognita       Meloidogyne incognita    Feb. 2008
                                        (M. incognita WS245/PRJEA28837/melInc2)
Microworm          Panagrellus redivivus    Feb. 2013           (Pred3/panRed1)
N. americanus      Necator americanus       Dec. 2013
                                                (WS242/N_americanus_v1/necAme1)
O. volvulus        Onchocerca volvulus      Nov. 2013
                                         (WS241/O_volvulus_Cameroon_v3/oncVol1)
P. exspectatus     Pristionchus exspectatus Mar. 2014
                                               (WS243/P_exspectatus_v1/priExs1)
P. pacificus       Pristionchus pacificus   Aug. 2014  (P_pacificus-v2/priPac3)
Pig roundworm      Ascaris suum             Sep. 2012
                                                    (WS229/AscSuum_1.0/ascSuu1)
Pine wood nematode Bursaphelenchus xylophilus Nov. 2011 
                                            (WS229/B. xylophilus Ka4C1/burXyl1)
Threadworm         Strongyloides ratti      Sep. 2014  (S. ratti ED321/strRat2)
Trichinella        Trichinella spiralis     Jan. 2011
                                     (WS225/Trichinella_spiralis-3.7.1/triSpi1)
Whipworm           Trichuris suis           Jul. 2014 (WS243/T. suis
                                                       DCEP-RM93M male/triSui1)

---------------------------------------------------------------
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.
There is approximately 152 Mb of compressed data in this directory.

Via rsync:
rsync -avz --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/ce11/phastCons26way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/ce11/phastCons26way

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)

---------------------------------------------------------------
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt23-Mar-2016 12:54 5.8K 
[   ]ce11.phastCons26way.bw08-Sep-2015 11:48 153M 
[SND]ce11.phastCons26way.mod18-Aug-2015 17:00 1.0K 
[   ]ce11.phastCons26way.wigFix.gz08-Sep-2015 11:47 72M 
[TXT]md5sum.txt09-Sep-2015 15:12 179  

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