This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/ce11/phyloP26way/README.txt This directory contains conversation scoring by phyloP (phylogenetic p-values) from the PHAST package (http://compgen.bscb.cornell.edu/phast/) 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 ce11.phyloP26way.bw - 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: http://hgdownload.cse.ucsc.edu/goldenPath/ce11/multiz26way/ For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=ce11&g=cons26way For a description of the phyloP wigFix 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 113 Mb of compressed data in this directory. Via rsync: rsync -avz --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/ce11/phyloP26way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/ce11/phyloP26way To download multiple files from the UNIX command line, use the "mget" command. mget ... - 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) ---------------------------------------------------------------