This file is from: http://hgdownload-test.cse.ucsc.edu/goldenPath/mm10/multiz4way/README.txt This directory contains compressed multiple alignments of the following assemblies to the mouse genome (mm10, Dec. 2011): Assemblies used in these alignments: Mouse Mus musculus Dec. 2011 (GRCm38/mm10) (reference) Malayan flying lemur Galeopterus variegatus Jun. 2014 (WashU/galVar1) Human Homo sapiens Dec. 2013 (GRCh38/hg38) Chinese tree shrew Tupaia chinensis Jan. 2013 (BGI/tupChi1) These alignments were prepared using the methods described in the track description file: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm10&g=cons4way based on the phylogenetic tree: mm10.4way.nh. Files in this directory: - mm10.4way.nh - phylogenetic tree used during the multiz multiple alignment - mm10.4way.commonNames.nh - same as mm10.4way.nh with the UCSC database names replaced by the common name for the species - mm10.4way.scientificName.nh - same as mm10.4way.nh with the UCSC database names replaced by the scientific name for the species - mm10.4way.maf.gz - the multiple alignments on the mouse genome - md5sum.txt - md5 check sums of these files to verify correct download files The mm10.4way.maf.gz file contain all the alignments for the chromosomes in the mouse genome, including additional annotations to indicate gap context and genomic breaks for the sequence in the underlying genome assemblies. Note, the compressed data size of the maf file is 2.0 Gb, uncompressed is 7.1 Gb. 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-test.cse.ucsc.edu/goldenPath/mm10/phastCons4way PhyloP conservation scores for these alignments are available at: http://hgdownload-test.cse.ucsc.edu/goldenPath/mm10/phyloP4way --------------------------------------------------------------- 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 2.1 Gb of compressed data in this directory. Via rsync: rsync -av --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/mm10/multiz4way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/mm10/multiz4way 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.