This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz20way/README.txt 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 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 --------------------------------------------------------------- These alignments were prepared using the methods described in the track description file: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons20way based on the phylogenetic tree: hg38.20way.nh Files in this directory: - hg38.20way.nh - phylogenetic tree used during the multiz multiple alignment - hg38.20way.commonNames.nh - same as hg38.20way.nh with the UCSC database name replaced by the common name for the species - hg38.20way.scientificNames.nh - same as hg38.20way.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_20-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 12 Gb, uncompressed is approximately 91 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/phastCons20way PhyloP conservation scores for these alignments are available at: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP20way --------------------------------------------------------------- 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 31 Gb of compressed data in this directory. Via rsync: rsync -avz --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz20way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/hg38/multiz20way To download multiple files from the UNIX command line, use the "mget" command. mget ... - 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. ---------------------------------------------------------------