This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/calJac3/phyloP13way/README.txt This directory contains conservation scoring by phyloP (phylogenetic p-values) from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple alignments of 12 vertebrate genomes to the marmoset genome. of scores for the primate species and the placental mammal species in the alignments. Files in this directory are: all.mod phyloP tree model with branch lengths for all 13 species: marmoset (calJac3) human (hg19) Baboon (papHam1) Bushbaby (otoGar1) Chimp (panTro2) Dog (canFam2) Gorilla (gorGor2) Mouse (mm9) Opossum (monDom5) Orangutan (ponAbe2) Rhesus (rheMac2) Mouse (micMur1) Tarsier (tarSyr1) vertebrate/*.wigFix.gz phyloP scores for all 13 species The multiple alignments and methods description are at: http://hgdownload.cse.ucsc.edu/goldenPath/calJac3/multiz13way/ For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=calJac3&g=cons13way --------------------------------------------------------------- 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: rsync -avz --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/calJac3/phyloP13way/ ./ OR ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/calJac3/phyloP13way 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)