This file is from:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz30way/README.txt
This directory contains compressed multiple alignments of the
following assemblies to the human genome (hg38/GRCh38, Dec. 2013):
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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)
---------------------------------------------------------------
These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons30way
based on the phylogenetic tree: hg38.30way.nh
Files in this directory:
- hg38.30way.nh - phylogenetic tree used during the multiz multiple alignment
- hg38.30way.commonNames.nh - same as hg38.30way.nh with the UCSC database
name replaced by the common name for the species
- hg38.30way.scientificNames.nh - same as hg38.30way.nh with the UCSC database
name replaced by the scientific name for the species
- upstream1000.knownGene.maf.gz - alignments in regions upstream, see below
- upstream2000.knownGene.maf.gz - alignments in regions upstream, see below
- upstream5000.knownGene.maf.gz - alignments in regions upstream, see below
- md5sum.txt - MD5 sum of the files to verify downloads
See also:
http://genomewiki.ucsc.edu/index.php/Hg38_30-way_conservation_alignment
The "alignments" directory contains compressed FASTA alignments
for the UCSC Known Gene CDS regions of the human genome
(hg38, Dec. 2013) aligned to the assemblies. Additional
alignment files are provided for RefSeq genes, and the
UCSC Known Gene canonical genes.
The "maf" directory contains the alignments to
the human assembly, with additional annotations to
indicate gap context, and genomic breaks for the
sequence in the underlying genome assemblies. Beware, the compressed
data size of the files in the 'maf' directory is 18 Gb,
uncompressed is approximately 158 Gb.
The upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for UCSC Known Genes with annotated 5' UTRs.
These files differ from the standard MAF format: they display
alignments that extend from start to end of the upstream region in
mouse, whether or not alignments actually exist. In situations where no
alignments exist or the alignments of one or more species are missing,
dot (".") is used as a placeholder. Multiple regions of an assembly's
sequence may align to a single region in the human sequence; therefore,
only the species name is displayed in the alignment data and no position
information is recorded. The alignment score is always zero in these files.
For a description of multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html.
PhastCons conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phastCons30way
PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP30way
---------------------------------------------------------------
Note, the uncompressed maf/*.maf.gz files are 158 Gb of data, when compressed,
they are approximately 18 Gb of compressed data. The entire set of
data in this directory is approximately 20 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.
Via rsync:
rsync -avz --progress \
rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz30way/ ./
Via FTP:
ftp hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/hg38/multiz30way
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.
---------------------------------------------------------------
All the files in this directory are freely usable for any
purpose. For data use restrictions regarding the individual
genome assemblies, see http://genome.ucsc.edu/goldenPath/credits.html.
---------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
upstream5000.knownGene.maf.gz 2017-11-06 12:55 1.0G
upstream2000.knownGene.maf.gz 2017-11-06 12:15 430M
upstream300.knownGene.maf.gz 2017-11-06 11:46 50M
hg38.30way.scientificNames.nh 2017-11-06 13:07 1.3K
hg38.30way.commonNames.nh 2017-11-06 13:07 1.1K
hg38.30way.nh 2017-11-06 13:07 1.1K
md5sum.txt 2017-11-07 13:41 363
maf/ 2017-11-06 14:26 -
alignments/ 2019-11-06 14:40 -