This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/phastCons7way/README.txt This directory contains compressed phastCons scores for multiple alignments of 6 yeast genomes to the the S. cerevisiae genome (sacCer3, April 2011): Files in this directory: sacCer3.7way.tree.mod - phastCons tree model with branch lengths for all 7 species sacCer3.chr*.wigFixed.gz - phastCons scores for the 7 species, wiggle fixed step format sacCer3.phastCons7way.bw phastCons scores for the 7 species in bigWig format md5sum.txt - md5 check sums of these files to verify correct download files The multiple alignments and methods description are at: http://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/multiz7way/ For a description of the phastCons data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html http://genome.ucsc.edu/goldenPath/help/wiggle.html Assemblies used in these alignments: - S. cerevisiae S. cerevisiae - S. paradoxus S. paradoxus - S. mikatae S. mikatae - S. kudriavzevii S. kudriavzevii - S. bayanus S. bayanus - S. castelli S. castelli - S. kluyveri S. kluyveri --------------------------------------------------------------- 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 100 Mb of data in this directory when uncompressed. Via rsync: rsync -av --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/phastCons7way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/sacCer3/phastCons7way 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)