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)
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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: <your email address>
go to the directory goldenPath/galGal6/phyloP35way
To download multiple files from the UNIX command line, use the "mget" command.
mget <filename1> <filename2> ...
- 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.
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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)
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Name Last modified Size Description
Parent Directory -
md5sum.txt 2020-12-23 15:13 109
mm39.35way.phyloP/ 2021-01-27 15:50 -
mm39.phyloP35way.bw 2020-12-22 18:52 5.7G
mm39.phyloP35way.mod 2020-12-22 13:57 1.3K