This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP17way/README.txt This directory contains conservation scoring by phyloP (phylogenetic p-values) from the PHAST package (http://compgen.cshl.edu/phast/) for multiple alignments of 16 primate genomes to the human genome. Files in this directory: hg38.phyloP17way.mod - phyloP tree model with branch lengths for all 17 species hg38.phyloP17way.bw - scores in bigWig format hg38.phyloP17way.wigFix.gz - scores in fixed step wiggle format md5sum.txt - MD5 checksums to verify download files See also: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1 for bigWig format description For a description of the fixed step wiggle data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html The phastCons data can be found at: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phastCons17way/ The multiple alignments and methods description are at: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz17way/ For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons17way Assemblies used in these alignments: (alignment type) Human - Homo sapiens Dec. 2013 (GRCh38/hg38) reference Baboon - Papio anubis Mar. 2012 (Baylor Panu_2.0/papAnu2) syntenic Bushbaby - Otolemur garnettii Mar. 2011 (Broad/otoGar3) reciprocal best Bonobo - Pan paniscus May. 2012 (Max-Planck/panPan1) reciprocal best Chimp - Pan troglodytes Feb. 2011 (CSAC 2.1.4/panTro4) syntenic Crab-eating macaque - Macaca fascicularis Jun 2013 (Macaca_fascicularis_5.0/macFas5) syntenic Gibbon - Nomascus leucogenys Oct. 2012 (GGSC Nleu3.0/nomLeu3) syntenic Golden snub-nosed monkey - Rhinopithecus roxellana Oct. 2014 (Rrox_v1/rhiRox1) reciprocal best Gorilla - Gorilla gorilla gorilla May 2011 (gorGor3.1/gorGor3) reciprocal best Green monkey - Chlorocebus sabaeus Mar. 2014 (Chlorocebus_sabeus 1.1/chlSab2) syntenic Marmoset - Callithrix jacchus Mar. 2009 (WUGSC 3.2/calJac3) syntenic Mouse lemur - Microcebus murinus Jul. 2007 (Broad/micMur1) reciprocal best Orangutan - Pongo pygmaeus abelii July 2007 (WUGSC 2.0.2/ponAbe2) syntenic Proboscis monkey - Nasalis larvatus Nov. 2014 (Charlie1.0/nasLar1) reciprocal best Rhesus - Macaca mulatta Oct. 2010 (BGI CR_1.0/rheMac3) syntenic Squirrel monkey - Saimiri boliviensis Oct. 2011 (Broad/saiBol1) reciprocal best Tarsier - Tarsius syrichta Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) reciprocal best --------------------------------------------------------------- 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/hg38/phyloP17way/ ./ OR ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/hg38/phyloP17way 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. 2010 Jan;20(1):110-21. (http://genome.cshlp.org/content/20/1/110.long) 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://genome.cshlp.org/content/15/8/1034.full) ---------------------------------------------------------------