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
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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)
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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: <your email address>
go to the directory goldenPath/hg38/phyloP30way
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 -
hg38.30way.phyloP/ 2017-11-07 13:27 -
hg38.phyloP30way.bw 2017-11-06 13:42 7.8G
hg38.phyloP30way.mod 2017-11-06 10:43 1.2K
md5sum.txt 2017-11-07 11:33 109