This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/mm10/phastCons4way/README.txt This directory contains compressed phastCons scores for multiple alignments of 3 genomes to the mouse genome (mm10, Dec. 2011): Files in this directory are: mm10.phastCons4way.mod phastCons tree model with branch lengths for the 4 species mm10.phastCons4way.wigFix.gz - phastCons scores for the 4 species in fixed step wiggle format mm10.phastCons4way.bw - phastCons scores for all 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 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: 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 4.3 Gb of compressed data in this directory. Via rsync: rsync -avz --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/mm10/phastCons4way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/mm10/phastCons4way 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) ---------------------------------------------------------------