This file is from: http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/phyloP7way/README.txt This directory contains conservation scoring by phyloP (phylogenetic p-values) from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple alignments of 7 coronavirus sequences. Files in this directory: md5sum.txt - md5 sums to verify copied files wuhCor1.7way.nameList.txt - relating the accession name to sequence name, and sample collection date wuhCor1.phyloP7way.mod - phyloP tree model with branch lengths for all 7 sequences wuhCor1.phyloP7way.bw - scores in bigWig format wuhCor1.phyloP7way.wigFix.gz - scores in fixed step wiggle format See also: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1 for bigWig format description For a description of the fixed step wiggle data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html The phastCons data can be found at: http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/phastCons7way/ The multiple alignments and methods description are at: http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/multiz7way/ For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=wuhCor1&g=cons7way --------------------------------------------------------------- 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: rsync -avz --progress \ rsync://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/phyloP7way/ ./ OR ftp hgdownload.soe.ucsc.edu user name: anonymous password: <your email address> go to the directory goldenPath/wuhCor1/phyloP7way 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 available for public use. For data use restrictions regarding the genome assemblies used in this annotation, see http://genome.ucsc.edu/goldenPath/credits.html. --------------------------------------------------------------- References for phastCons and phyloP: Pollard KS, Hubisz MJ, Siepel A. Detection of non-neutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. (http://genome.cshlp.org/content/20/1/110.long) Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. (http://genome.cshlp.org/content/15/8/1034) ---------------------------------------------------------------
Name Last modified Size Description
Parent Directory - UShER_SARS-CoV-2/ 2024-01-02 19:28 - bigZips/ 2024-02-29 14:27 - chromosomes/ 2020-02-07 10:29 - database/ 2024-09-01 04:18 - liftOver/ 2022-01-07 15:08 - multiz7way/ 2020-05-19 13:12 - multiz44way/ 2020-03-26 15:37 - multiz119way/ 2020-05-01 14:55 - pangolin-assignment/ 2022-12-12 08:59 - phastCons44way/ 2020-03-26 15:37 - phastCons119way/ 2020-05-01 14:55 - phyloP44way/ 2020-03-26 15:37 - phyloP119way/ 2020-05-01 14:55 - vaccines/ 2021-05-11 14:37 - md5sum.txt 2021-01-06 16:01 281 wuhCor1.7way.nameList.txt 2020-05-19 13:03 289 wuhCor1.phyloP7way.mod 2021-01-06 15:46 474 wuhCor1.phastCons7way.mod 2021-01-06 15:41 497 wuhCor1.phastCons7way.wigFix.gz 2021-01-06 15:42 33K wuhCor1.phyloP7way.wigFix.gz 2021-01-06 15:47 39K wuhCor1.phastCons7way.bw 2021-01-06 15:42 108K wuhCor1.phyloP7way.bw 2021-01-06 15:47 109K