This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/ce9/phyloP10way/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 9 nematode genomes to the C. elegans genome, plus an alternate set of scores for the five Caenorhabditis subset of species in the alignments. Files in this directory are: README.txt caenorhabditis.mod phyloP tree model with branch lengths for the five Caenorhabditis species nematode.mod phyloP tree model with branch lengths for all 10 nematode species phyloP10way.caenorhabditis.wigFix.gz - phyloP scores for the five Caenorhabditis species phyloP10way.wigFix.gz - phyloP scores for all 10 nematode species md5sum.txt - md5 sums of the above 4 files to verify accurate download The multiple alignments and methods description are at: http://hgdownload.cse.ucsc.edu/goldenPath/ce9/multiz10way/ For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=ce9&g=cons10way 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: - Caenorhabditis elegans Jan. 2010 ce9/WS210 - Caenorhabditis briggsae Jan. 2007 cb3/WS210/WUGSC 1.0 - Caenorhabditis remanei May 2007 caeRem3/WS210/WUGSC 15.0.1 - Caenorhabditis brenneri Feb. 2008 caePb2/WS210/WUGSC 6.0.1 - Caenorhabditis japonica Sep. 2010 caeJap3/WUGSC 7.0.1 - Haemonchus contortus Dec. 2009 haeCon1/WS210 - Pristionchus pacificus Dec. 2008 priPac2/WUGSC 5.0.1 - Meloidogyne hapla VW9 Sep. 2008 melHap1/WS210 - Meloidogyne incognita Feb. 2008 melInc1/WS210 - Brugia malayi Sep. 2007 bruMal1/WS210/TIGR 1.0 --------------------------------------------------------------- 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/ce9/phyloP10way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/ce9/phyloP10way 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. 2009 Oct 26. [Epub ahead of print] (http://genome.cshlp.org/content/early/2009/10/26/gr.097857.109.abstract) 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://www.genome.org/cgi/doi/10.1101/gr.3715005)