This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP20way/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 19 genome sequences to the human genome.
Files in this directory:
hg38.phyloP20way.mod - phyloP tree model with branch lengths for
all 20 species
hg38.phyloP20way.bw - scores in bigWig format
hg38.phyloP20way.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/phastCons20way/
The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz20way/
For more information about this data, see the track
description for the Conservation track:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons20way
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 Jul. 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
Tree shrew - Tupaia belangeri Dec. 2006 (Broad/tupBel1) reciprocal best
Mouse - Mus musculus Dec. 2011 (GRCm38/mm10) syntenic
Dog - Canis lupus familiaris Sep. 2011 (Broad CanFam3.1/canFam3) syntenic
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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:
rsync -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP20way/ ./
OR
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/hg38/phyloP20way
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.phyloP20way.mod 2015-04-15 20:31 885
hg38.phyloP20way.wigFix.gz 2015-04-17 09:08 4.3G
hg38.phyloP20way.bw 2015-04-17 10:53 7.3G
md5sum.txt 2015-04-17 12:02 170