This directory contains compressed phastCons scores for multiple alignments of 30 vertebrate genomes to the mouse genome, plus an alternate set of scores for the euchontoglires subset of species in the alignments, and an alternate set of scores for the placental mammal subset of species in the alignments. Files in this directory are: vertebrate.mod phastCons tree model with branch lengths for all 30 species euarchontoglires.mod phastCons tree model for the euarchontoglires subset placental.mod phastCons tree model for the placental subset vertebrate/*.data.gz phastCons scores for 30 species euarchontoglires/*.data.gz phastCons scores for placental subset (11 species) placental/*.data.gz phastCons scores for placental subset (20 species) The multiple alignments and methods description are at: http://hgdownload.cse.ucsc.edu/goldenPath/mm9/multiz30way/ 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/mm9/phastCons30way 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).