This directory contains compressed phastCons scores for multiple alignments of 5 other vertebrate genomes to the lamprey genome: - lamprey Petromyzon marinus June 2007, petMar1 reference - human Homo sapiens Mar 2006, hg18 recip best net - mouse Mus musculus July 2007, mm9 recip best net - chicken Gallus gallus May 2006, galGal3 recip best net - medaka Oryzias latipes Apr 2006, oryLat1 recip best net - Lancelet Branchiostoma floridae Mar 2006, braFlo1 recip best net Files in this directory are: 6way.mod phastCons tree model with branch lengths for the 6 species file_*.data.gz - phastCons scores for the 6 species each file contains the data for a number of contigs for Lamprey The multiple alignments and methods description are at: http://hgdownload.cse.ucsc.edu/goldenPath/petMar1/multiz6way/ 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/petMar1/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. Checksum values for all files in this directory can be found in md5sum.txt. --------------------------------------------------------------- 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).