This file is from: http://hgdownload.soe.ucsc.edu/goldenPath/mm39/phyloP35way/README.txt This directory contains conversation scoring by phyloP (phylogenetic p-values) from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple alignments of 34 genomes to the mouse mm39/Jun. 2020 genome. Files in this directory are: mm39.phyloP35way.mod phyloP tree model with branch lengths for all the sequences mm39.35way.phyloP/*.wigFix.gz - phyloP scores for all the alignments in fixed step wiggle format mm39.phyloP35way.bw - phyloP scores for all the alignments in bigWig format md5sum.txt - md5 sums of the files here to verify accurate download The multiple alignments and methods description are at: http://hgdownload.soe.ucsc.edu/goldenPath/mm39/multiz35way/ For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm39&g=cons35way For a description of the phyloP wigFix data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html see also the section describing the 'fixedStep' wiggle format: http://genome.ucsc.edu/goldenPath/help/wiggle.html Assemblies used in these alignments: Mouse - Mus musculus Jun. 2020 (GRCm39/mm39) (reference) Beaver - Castor canadensis Feb. 2017 (C.can genome v1.0/casCan1) (reciprocal best) Bonobo - Pan paniscus May 2020 (Mhudiblu_PPA_v0/panPan3) (syntenic) Bushbaby - Otolemur garnettii Mar. 2011 (Broad/otoGar3) (reciprocal best) Chicken - Gallus gallus Mar. 2018 (GRCg6a/galGal6) (maf net) Chimp - Pan troglodytes Jan. 2018 (Clint_PTRv2/panTro6) (syntenic) Chinese hamster - Cricetulus griseus Jun. 2020 (GCF_0003668045.3 CriGri-PICRH-1.0) (syntenic) Chinese pangolin - Manis pentadactyla Aug 2014 (M_pentadactyla-1.1.1/manPen1) (reciprocal best) Cow - Bos taurus Apr. 2018 (ARS-UCD1.2/bosTau9) (reciprocal best) Dog - Canis lupus familiaris Mar. 2020 (UU_Cfam_GSD_1.0/canFam4) (syntenic) Dolphin - Tursiops truncatus Oct. 2011 (Baylor Ttru_1.4/turTru2) (reciprocal best) Elephant - Loxodonta africana Jul. 2009 (Broad/loxAfr3) (reciprocal best) Gorilla - Gorilla gorilla gorilla Aug. 2019 (Kamilah_GGO_v0/gorGor6) (syntenic) Guinea pig - Cavia porcellus Feb. 2008 (Broad/cavPor3) (syntenic) Hawaiian monk seal - Neomonachus schauinslandi Jun. 2017 (ASM220157v1/neoSch1) (syntenic) Hedgehog - Erinaceus europaeus May 2012 (EriEur2.0/eriEur2) (reciprocal best) Horse - Equus caballus Jan. 2018 (EquCab3.0/equCab3) (syntenic) Human - Homo sapiens Dec. 2013 (GRCh38/hg38) (syntenic) Lamprey - Petromyzon marinus Dec. 2017 (Pmar_germline 1.0/petMar3) (maf net) Malayan flying lemur - Galeopterus variegatus Jun. 2014 (G_variegatus-3.0.2/galVar1) (maf net) Marmoset - Callithrix jacchus May 2020 (Callithrix_jacchus_cj1700_1.1/calJac4) (syntenic) Opossum - Monodelphis domestica Oct. 2006 (Broad/monDom5) (maf net) Pig - Sus scrofa Aug. 2011 (SGSC Sscrofa10.2/susScr3) (reciprocal best) Pika - Ochotona princeps May 2012 (OchPri3.0/ochPri3) (reciprocal best) Rabbit - Oryctolagus cuniculus Apr. 2009 (Broad/oryCun2) (reciprocal best) Rat - Rattus norvegicus Jul. 2014 (RGSC 6.0/rn6) (syntenic) Rhesus - Macaca mulatta Feb. 2019 (Mmul_10/rheMac10) (syntenic) Sheep - Ovis aries Nov. 2015 (Oar_v4.0/oviAri4) (syntenic) Shrew - Sorex araneus Aug. 2008 (Broad/sorAra2) (reciprocal best) Squirrel - Spermophilus tridecemlineatus Nov. 2011 (Broad/speTri2) (reciprocal best) Tarsier - Tarsius syrichta Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) (reciprocal best) Tenrec - Echinops telfairi Nov. 2012 (Broad/echTel2) (reciprocal best) Tree shrew - Tupaia belangeri Dec. 2006 (Broad/tupBel1) (reciprocal best) X. tropicalis - Xenopus tropicalis Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9) (maf net) Zebrafish - Danio rerio May 2017 (GRCz11/danRer11) (maf net) --------------------------------------------------------------- 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. There is approximately 9.1 Gb of compressed data in this directory, approximately 18.6 Gb uncompressed.. Via rsync: rsync -avz --progress \ rsync://hgdownload.soe.ucsc.edu/goldenPath/galGal6/phyloP35way/ ./ Via FTP: ftp hgdownload.soe.ucsc.edu user name: anonymous password: go to the directory goldenPath/galGal6/phyloP35way 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) ---------------------------------------------------------------