This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz5way/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 Malayan flying lemur - Galeopterus variegatus Jun. 2014 (WashU 3.0.2/galVar1) syntenic Chinese tree shrew - Tupia chinensis Jan. 2013 (BGI CR_1.0/tupChi1) syntenic Guinea pig - Cavia porcellus Feb. 2008 (Broad/cavPor3) syntenic Mouse - Mus musculus Dec. 2011 (GRCm38/mm10) syntenic --------------------------------------------------------------- These alignments were prepared using the methods described in the track description file: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons5way based on the phylogenetic tree: hg38.5way.nh Files in this directory: - hg38.5way.nh - phylogenetic tree used during the multiz multiple alignment - hg38.5way.commonNames.nh - same as hg38.5way.nh with the UCSC database name replaced by the common 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 - hg38.5way.maf.gz - alignmens with gap annotation See also: http://genomewiki.ucsc.edu/index.php/Hg38_5-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 hg38.5way.maf.gz file 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 this file is 3.2 Gb, uncompressed is approximately 13 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/phastCons5way PhyloP conservation scores for these alignments are available at: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP5way --------------------------------------------------------------- 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/multiz5way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/hg38/multiz5way 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. ---------------------------------------------------------------