This file is from:

    http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/multiz7way/README.txt

This directory contains compressed multiple alignments of 7 virus sequences.
These 7 sequences represent coronavirus strains in human populations

The 'reference' sequence for this collection is the sequence:

  NC_045512v2 - 2019-12-30 - Wuhan-Hu-1
  https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2

Description 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

  wuhCor1.7way.nh - Phylogenetic tree used for multiz alignment.
           The phylogenetic tree was calculated on 31mer frequency similarity
           and neighbor joining that distance matrix with the phylip toolset:
           http://evolution.genetics.washington.edu/phylip.html
           'neighbor' command:
           http://evolution.genetics.washington.edu/phylip/progs.data.dist.html

  wuhCor1.multiz7way.maf.gz - alignments with gap annotation with
                                accession identifiers

  dnaFasta7.fa.tgz - gzipped tar file for the DNA fasta, 7 sequences
                - to extract sequences: tar xvzf dnaFasta7.fa.tgz
                - creates seven files:
                # -rw-rw-r-- 1 27718 May 13 08:44 CoV229E.fa
                # -rw-rw-r-- 1 30361 May 13 08:44 HKU1.fa
                # -rw-rw-r-- 1 30557 May 13 08:44 MERS.fa
                # -rw-rw-r-- 1 27954 May 13 08:44 NL63.fa
                # -rw-rw-r-- 1 31188 May 13 08:44 OC43.fa
                # -rw-rw-r-- 1 30190 May 13 09:37 SARS_CoV_1.fa
                # -rw-rw-r-- 1 30515 May 13 08:49 wuhCor1.fa

   Example measurement of the sequences with the 'faCount' command:
#  faCount *.fa
#
#       #seq    len     A       C       G       T       N       cpg
#       CoV229E 27317   7420    4549    5903    9445    0       488
#       HKU1    29926   8331    3895    5699    12001   0       340
#       MERS    30119   7900    6116    6304    9799    0       711
#       NL63    27553   7253    3979    5516    10805   0       332
#       OC43    30741   8502    4660    6649    10930   0       485
#       SARS_CoV_1      29751   8481    5940    6187    9143    0       568
#       NC_045512v2     29903   8954    5492    5863    9594    0       439
#       total   205310  56841   34631   42121   71717   0       3363

For a description of multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html.

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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.

Via rsync:
rsync -avz --progress \
        rsync://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/multiz7way/ ./

Via FTP:
    ftp hgdownload.soe.ucsc.edu
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/wuhCor1/multiz7way

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.

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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.
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