This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/danRer6/phastCons6way/README.txt This directory contains compressed phastCons scores for multiple alignments of 6 vertebrate genomes to the zebrafish genome. Files in this directory are: all.mod phastCons tree model with branch lengths for all 6 species phastCons6way.wigFix.gz phastCons scores for 6 species The multiple alignments and methods description are at: http://hgdownload.cse.ucsc.edu/goldenPath/danRer6/multiz6way/ For a description of the phastCons data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html Assemblies used in these alignments: - Zebrafish Danio rerio Dec. 2008 danRer6 - Tetraodon Tetraodon nigroviridis Mar. 2007 tetNig2 - Stickleback Gasterosteus aculeatus Feb. 2006 gasAcu1 - X. tropicalis Xenopus tropicalis Aug. 2005 xenTro2 - Mouse Mus musculus July 2007 mm9 - Human Homo sapiens Feb. 2009 hg19/GRCh37 --------------------------------------------------------------- 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 333 MB of compressed data in this directory. Via rsync: rsync -avz --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer6/phastCons6way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/danRer6/phastCons6way 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)