This file is from: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus241way/README.txt This directory contains compressed multiple alignments of 241 mammalian species and measurements of evolutionary conservation from the Zoonomia Project This track shows multiple alignments of 241 vertebrate species and measurements of evolutionary conservation from the Zoonomia Project. https://zoonomiaproject.org/the-project/ The multiple alignments were generated using the Cactus comparative genomics alignment system. Cactus produces reference-free, whole-genome multiple alignments. https://github.com/ComparativeGenomicsToolkit/cactus/ The base-wise conservation scores are computed using phyloP from the PHAST package, for all species. This version was prepared by Michael Dong (Uppsala U) with an improved neutral model incorporating better versions of ancestral repeats. Please note the table of species in the description page for the track: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=cons241way ____________________________________________________________________________ Files in this directory: hg38.cactus241way.scientificNames.nh - phylogenetic tree used during the - cactus multiple alignment hg38.cactus241way.nh - some of the species translate to UCSC database - equivalents. Tree used for display in the genome - browser, identical to the scientificNames tree. hg38.cactus241way.phyloP.bw - PhyloP scores in bigWig format files: See also: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1 for bigWig format description hg38.cactus241way.phyloP.wigFix.gz - PhyloP scores in fixed step wiggle format md5sum.txt - md5sum checksums for the files in this directory For a description of the fixed step wiggle data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html The maf/chr*.maf.gz files each contain all the alignments to that particular human chromosome. Beware, the compressed data size of these files is about 1.2 Tb, uncompressed size is about 9.1 Tb. The maf/md5sum.txt - md5sum checksums for the files in the maf directory Please note the table of species in the description page for the track: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=cons241way ____________________________________________________________________________ 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 1.2 Tb of compressed data in this directory, uncompressed approximately 9.1 Tb. Via rsync: rsync -avz --progress \ rsync://hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus241way/ ./ Via FTP: ftp hgdownload.soe.ucsc.edu user name: anonymous password: <your email address> go to the directory goldenPath/hg38/cactus241way 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 - alignments/ 2022-04-19 17:10 - cactus241way.bigMaf 2021-09-13 10:40 1.1T cactus241way.phyloP.bw 2021-05-10 12:28 9.0G cactus241wayFrames.bb 2021-08-06 13:29 216M cactus241waySummary.bb 2022-08-23 17:13 21G hg38.cactus241way.frames.bb 2021-06-30 11:01 4.0M hg38.cactus241way.nh 2020-12-15 23:12 11K hg38.cactus241way.phyloP.bw 2021-05-10 12:28 9.0G hg38.cactus241way.phyloP.wigFix.gz 2021-05-10 11:22 5.4G hg38.cactus241way.scientificNames.nh 2020-12-15 22:39 11K maf/ 2021-05-14 11:40 - md5sum.txt 2021-05-14 12:07 257 phyloP241way/ 2022-12-08 15:37 -