This directory contains compressed phastCons scores for multiple alignments of 5 other nematode genomes to the C. elegans genome: - C. elegans May 2008, ce6 reference - C. remanei May 2007, caeRem3 chain net - C. briggsae Jan 2007, cb3 chain net - C. brenneri Feb 2008, caePb1 chain net - C. japonica Mar 2008, caeJap1 chain net - P. pacificus May 2007, priPac1 chain net Files in this directory are: 6way.conserved.mod phastCons conserved tree model 6way.non-conserved.mod phastCons non-conserved tree model chr*.data.gz - phastCons scores for the 6 species md5sum.txt - MD5 check sums for the *.data.gz and *.mod files The multiple alignments and methods description are at: http://hgdownload.cse.ucsc.edu/goldenPath/ce6/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/ce6/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: 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).