This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/mm10/phyloP4way/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 3 genomes to the mouse genome (mm10, Dec. 2011) Files in this directory are: mm10.phyloP4way.mod phyloP tree model with branch lengths for the 4 genomes mm10.phyloP4way.wigFix.gz - phyloP scores for the 4 genomes in fixed step wiggle format mm10.phyloP4way.bw - phyloP scores for the 4 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/mm10/multiz4way/ For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm10&g=cons4way 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: Mouse Mus musculus Dec. 2011 (GRCm38/mm10) (reference) Malayan flying lemur Galeopterus variegatus Jun. 2014 (WashU/galVar1) Human Homo sapiens Dec. 2013 (GRCh38/hg38) Chinese tree shrew Tupaia chinensis Jan. 2013 (BGI TupChi1_1.0/tupChi1) --------------------------------------------------------------- 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 3.6 Gb of compressed data in this directory. Via rsync: rsync -avz --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/mm10/phyloP4way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: <your email address> go to the directory goldenPath/mm10/phyloP4way 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) ---------------------------------------------------------------
Name Last modified Size Description
Parent Directory - mm10.phyloP4way.mod 2017-04-21 12:22 391 mm10.phyloP4way.wigFix.gz 2017-04-21 12:39 1.3G mm10.phyloP4way.bw 2017-04-21 15:04 2.3G md5sum.txt 2017-04-21 21:03 167