This directory contains compressed phastCons scores for multiple alignments of the following assemblies to the human genome (hg18, Mar. 2006): - chimp (Nov 2003, panTro1) - mouse (Feb 2006, mm8) - rat (Nov 2004, rn4) - rabbit (May 2005, oryCun1) - macaque (Jan 2006, rheMac2) - dog (May 2005, canFam2) - cow (Mar 2005, bosTau2) - armadillo (May 2005, dasNov1) - elephant (May 2005, loxAfr1) - tenrec (Jul 2005, echTel1) - opossum (Jan 2006, monDom4) - chicken (Feb 2004, galGal2) - frog (Oct 2004, xenTro1) - zebrafish (May 2005, danRer3) - tetraodon (Feb 2004, tetNig1) - fugu (Aug 2002, fr1) For a description of the phastCons file format, see http://genome.ucsc.edu/goldenPath/help/phastCons.html. ----------------------------------------------------------------- To download a large file or multiple files from this directory, we recommend that you use ftp rather than downloading the files via our website. To do so: ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/hg18/phastCons17way 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: Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S., Weinstock, G.M., Wilson, R. K., Gibbs, R.A., Kent, W.J., Miller, W., and Haussler, D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005). (http://www.genome.org/cgi/doi/10.1101/gr.3715005) Siepel, A. and Haussler, D. Phylogenetic hidden Markov models. In R. Nielsen, ed., Statistical Methods in Molecular Evolution, Springer (in press) (2004). For a discussion of the methods used to calculate the phastCons scores, see the description page for the hg17 Conservation track in the Genome Browser.