This file is from:

This directory contains conversation scoring by phyloP (phylogenetic p-values)
from the PHAST package ( for multiple
alignments of 26 nematode genomes to the C. elegans genome.

Files in this directory are:

    ce11.phyloP26way.mod  phyloP tree model with branch lengths
                        for the 26 nematodes
    ce11.phyloP26way.wigFix.gz - phyloP scores for the 26 nematodes
                                 in fixed step wiggle format - phyloP scores for the 26 nematodes species
                          in bigWig format
    md5sum.txt - md5 sums of the files here to verify accurate download

The multiple alignments and methods description are at:

For more information about this data, see the track
description for the Conservation track:

For a description of the phyloP wigFix data file format, see:
see also the section describing the 'fixedStep' wiggle format:

Assemblies used in these alignments:

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

A. ceylanicum      Ancylostoma ceylanicum   Mar. 2014
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
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
Filarial worm      Brugia malayi            May. 2014
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
O. volvulus        Onchocerca volvulus      Nov. 2013
P. exspectatus     Pristionchus exspectatus Mar. 2014
P. pacificus       Pristionchus pacificus   Aug. 2014  (P_pacificus-v2/priPac3)
Pig roundworm      Ascaris suum             Sep. 2012
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
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 113 Mb of compressed data in this directory.

Via rsync:
rsync -avz --progress \
	rsync:// ./

Via FTP:
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/ce11/phyloP26way

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

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.

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.  (

      Name                       Last modified      Size  Description
Parent Directory - 2015-09-08 12:42 172M ce11.phyloP26way.mod 2015-09-08 12:14 1.0K ce11.phyloP26way.wigFix.gz 2015-09-08 12:40 98M md5sum.txt 2015-09-09 15:18 170