This file is from:

This directory contains compressed multiple alignments of the 
following assemblies to the human genome (hg38/GRCh38, Dec. 2013):

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:
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:

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

PhastCons conservation scores for these alignments are available at:

PhyloP conservation scores for these alignments are available at:

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:// ./

Via FTP:
    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
      Name                          Last modified      Size  Description
Parent Directory - alignments/ 2019-11-06 14:40 - hg38.30way.commonNames.nh 2017-11-06 13:07 1.1K hg38.30way.nh 2017-11-06 13:07 1.1K hg38.30way.scientificNames.nh 2017-11-06 13:07 1.3K maf/ 2017-11-06 14:26 - md5sum.txt 2017-11-07 13:41 363 upstream300.knownGene.maf.gz 2017-11-06 11:46 50M upstream2000.knownGene.maf.gz 2017-11-06 12:15 430M upstream5000.knownGene.maf.gz 2017-11-06 12:55 1.0G