This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP30way/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 29 genome sequences to the human genome. Files in this directory: hg38.30way.phyloP/*.wigFix.gz - scores in fixed step wiggle format hg38.phyloP30way.mod - phyloP tree model with branch lengths for all 30 species hg38.phyloP30way.bw - scores in bigWig 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/phastCons30way/ The multiple alignments and methods description are at: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz30way/ For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons30way ----------------------------------------------------------------------------- Assemblies used in these alignments: (alignment type) Human - Homo sapiens Dec. 2013 (GRCh38/hg38) (reference) Angolan colobus - Colobus angolensis palliatus Mar. 2015 (Cang.pa_1.0/colAng1) (syntenic) Armadillo - Dasypus novemcinctus Dec. 2011 (Baylor/dasNov3) (syntenic) Baboon - Papio anubis Feb. 2013 (Baylor Panu_2.0/papAnu3) (reciprocal best) Black lemur - Eulemur macaco Aug. 2015 (Emacaco_refEf_BWA_oneround/eulMac1) (reciprocal best) Black snub-nosed monkey - Rhinopithecus bieti Aug. 2016 (ASM169854v1/rhiBie1) (reciprocal best) Bonobo - Pan paniscus Aug. 2015 (MPI-EVA panpan1.1/panPan2) (syntenic) Bushbaby - Otolemur garnettii Mar. 2011 (Broad/otoGar3) (syntenic) Chimp - Pan troglodytes May 2016 (Pan_tro 3.0/panTro5) (syntenic) Coquerel's sifaka - Propithecus coquereli Mar. 2015 (Pcoq_1.0/proCoq1) (syntenic) Crab-eating macaque - Macaca fascicularis Jun. 2013 (Macaca_fascicularis_5.0/macFas5) (syntenic) Dog - Canis lupus familiaris Sep. 2011 (Broad CanFam3.1/canFam3) (syntenic) Drill - Mandrillus leucophaeus Mar. 2015 (Mleu.le_1.0/manLeu1) (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 Mar. 2016 (GSMRT3/gorGor5) (syntenic) Green monkey - Chlorocebus sabaeus Mar. 2014 (Chlorocebus_sabeus 1.1/chlSab2) (syntenic) Ma's night monkey - Aotus nancymaae Jun. 2017 (Anan_2.0/aotNan1) (syntenic) Marmoset - Callithrix jacchus March 2009 (WUGSC 3.2/calJac3) (syntenic) Mouse - Mus musculus Dec. 2011 (GRCm38/mm10) (syntenic) Mouse lemur - Microcebus murinus Feb. 2017 (Mmur_3.0/micMur3) (syntenic) Orangutan - Pongo pygmaeus abelii July 2007 (WUGSC 2.0.2/ponAbe2) (reciprocal best) Pig-tailed macaque - Macaca nemestrina Mar. 2015 (Mnem_1.0/macNem1) (syntenic) Proboscis monkey - Nasalis larvatus Nov. 2014 (Charlie1.0/nasLar1) (reciprocal best) Rhesus - Macaca mulatta Nov. 2015 (BCM Mmul_8.0.1/rheMac8) (syntenic) Sclater's lemur - Eulemur flavifrons Aug. 2015 (Eflavifronsk33QCA/eulFla1) (reciprocal best) Sooty mangabey - Cercocebus atys Mar. 2015 (Caty_1.0/cerAty1) (syntenic) Squirrel monkey - Saimiri boliviensis Oct. 2011 (Broad/saiBol1) (syntenic) Tarsier - Tarsius syrichta Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) (reciprocal best) White-faced sapajou - Cebus capucinus imitator Apr. 2016 (Cebus_imitator-1.0/cebCap1) (syntenic) ----------------------------------------------------------------------------- Note, the uncompressed *.wigFix.gz files are 18 Gb of data, when compressed, they are approximately 4.6 Gb of compressed data. The entire set of data in this directory is approximately 13 Gb. 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/phyloP30way/ ./ OR ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/hg38/phyloP30way 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) ---------------------------------------------------------------