This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/phastCons11way/README.txt This directory contains compressed phastCons scores for multiple alignments of 10 vertebrate genomes to the Gorilla genome. Files in this directory are: primate.mod - phastCons tree model with branch lengths for all 11 species: gorilla, chimp, human, gibbon, orangutan, baboon, rhesus, marmoset, tarsier, mouse lemur, bushbaby (gorGor3, panTro3, hg19, nomLeu1, ponAbe2, papHam1, rheMac2, calJac3, tarSyr1, micMur1, otoGar1) phastCons11way.wigFix.gz phastCons scores for 11 species, wiggle fixed step phastCons11way.bw phastCons scores for 11 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/gorGor3/multiz11way/ For a description of the phastCons data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html Assemblies used in these alignments: Gorilla gorilla gorilla May 2011 Sanger gorGor3.1/gorGor3 Chimp Pan troglodytes Oct. 2010 CGSC 2.1.3/panTro3 Human Homo sapiens Feb. 2009 GRCh37/hg19 Gibbon Nomascus leucogenys Jan. 2010 GGSC Nleu1.0/nomLeu1 Orangutan Pongo pygmaeus abelii Jul. 2007 WUGSC 2.0.2/ponAbe2 Baboon Papio hamadryas Nov. 2008 Baylor 1.0/papHam1 Rhesus Macaca mulatta Jan. 2006 MGSC Merged 1.0/rheMac2 Marmoset Callithrix jacchus Mar. 2009 WUGSC 3.2/calJac3 Tarsier Tarsius syrichta Aug. 2008 Broad/tarSyr1 Mouse lemur Microcebus murinus Jun. 2003 Broad/micMur1 Bushbaby Otolemur garnettii Dec. 2006 Broad/otoGar1 --------------------------------------------------------------- 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 910 Mb of compressed data in this directory. Via rsync: rsync -av --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/gorGor3/phastCons11way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/gorGor3/phastCons11way 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)