This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/hg38/cactus447way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the human genome (hg38/GRCh38, Dec. 2013):

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Assemblies used in these alignments:         (alignment type)

Human - Homo sapiens
                Dec. 2013 (GRCh38/hg38) (reference)

---------------------------------------------------------------

This alignment was created by making three edits (using Cactus)
to the 241-way mammalian Zoonomia Cactus alignment
   ( https://cglgenomics.ucsc.edu/data/cactus/).

1. One additional cat genome, "Felis_catus_fca126" (GCA_018350175.1) was
   added as a sister taxa to the existing "Felis_catus" species
2. Five additional canine genomes were also added: canFam4, "Canis_lupus_dingo"
   (GCA_003254725.1), "Canis_lupus_orion" (GCA_905319855.2),
   "Nyctereutes_procyonoides" (GCA_905146905.1) and
   "Otocyon_megalotis" (GCA_017311455.1). "Canis_lupus" from the
    Zoonomia alignment was also renamed "Canis_lupus_VD" to reflect the
    fact that it corresponds to a "village dog" and not "wolf" sample.
3. The 43-species primates clade from the Zoonomia alignment was removed and
   replaced with the 243-way primates alignment from
   TODO: [CITE ILLUMINA PAPER], increasing the alignment by
   200 additional primate species.

Phylogenic tree

The phylogenic tree was established by the research described in the paper:
Lukas F. K. Kuderna, et al. A global catalog of whole-genome diversity from
233 primate species. Science Vol. 380, No. 6648, 906-913 (2023),
DOI: 10.1126/science.abn7829 

Files in this directory:
 - hg38.447way.nh.txt - phylogenetic tree used to guide the cactus alignment
 - hg38.447way.commonNames.nh.txt - same tree with the common names
 - cactus447wayFrames.bb - the reading frames for display of amino acid coding
                           regions in the display at base level
 - cactus447waySummary.bb - a bigBed format file for a pre-calculated display
                          - of the maf coverage graph when viewing larger areas
 - hg38.cactus447way.bb - the maf file data in bigMaf file format for use
                          in the display of the track in the genome browser

 - md5sum.txt - MD5 sum of the files to verify downloads

    See also:

The "maf" directory 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 the files in the 'maf' directory is 7.4 Tb,
uncompressed here is approximately 1.5 Tb.

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

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/phyloP447way

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Note, the uncompressed maf/*.maf.gz files are 7.4 Tb of data, when compressed, 
they are approximately 1.5 Tb of compressed data.  The entire set of
data in this directory is approximately 4.1 Tb.

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.cse.ucsc.edu/goldenPath/hg38/cactus447way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg38/cactus447way

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 - hg38.447way.commonNames.nh.txt 2023-10-16 15:53 22K hg38.447way.scientificNames.nh.txt 2023-10-16 15:48 22K hg38.447way.nh.txt 2023-10-16 15:45 22K cactus447waySummary.bb 2023-10-16 15:28 1.0G cactus447wayFrames.bb 2023-10-16 15:12 159M maf/ 2023-10-01 22:34 - hg38.cactus447way.bb 2023-06-29 19:48 1.5T