This directory contains compressed FASTA alignments for the CDS regions
of the human genome (hg38/GRCh38, Dec. 2013) aligned to the 
following assemblies:

Assemblies used in these alignments:                                 (alignment
                                                                           type)

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

Baboon - Papio anubis              Mar. 2012 (Baylor Panu_2.0/papAnu2)  syntenic
Bushbaby - Otolemur garnettii      Mar. 2011 (Broad/otoGar3)     reciprocal best
Bonobo - Pan paniscus             May. 2012 (Max-Planck/panPan1) reciprocal best
Chimp - Pan troglodytes            Feb. 2011 (CSAC 2.1.4/panTro4)      syntenic
Crab-eating macaque - Macaca fascicularis
                          Jun 2013 (Macaca_fascicularis_5.0/macFas5)  syntenic
Gibbon - Nomascus leucogenys       Oct. 2012 (GGSC Nleu3.0/nomLeu3)    syntenic
Golden snub-nosed monkey - Rhinopithecus roxellana
                          Oct. 2014 (Rrox_v1/rhiRox1)           reciprocal best
Gorilla - Gorilla gorilla gorilla  May 2011 (gorGor3.1/gorGor3) reciprocal best
Green monkey - Chlorocebus sabaeus
                          Mar. 2014 (Chlorocebus_sabeus 1.1/chlSab2)  syntenic
Marmoset - Callithrix jacchus      Mar. 2009 (WUGSC 3.2/calJac3)     syntenic
Mouse lemur - Microcebus murinus   Jul. 2007 (Broad/micMur1) reciprocal best
Orangutan - Pongo pygmaeus abelii  Jul. 2007 (WUGSC 2.0.2/ponAbe2)   syntenic
Proboscis monkey - Nasalis larvatus
                          Nov. 2014 (Charlie1.0/nasLar1)        reciprocal best
Rhesus - Macaca mulatta            Oct. 2010 (BGI CR_1.0/rheMac3)      syntenic
Squirrel monkey - Saimiri boliviensis Oct. 2011 (Broad/saiBol1) reciprocal best
Tarsier - Tarsius syrichta
                   Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) reciprocal best
Tree shrew - Tupaia belangeri      Dec. 2006 (Broad/tupBel1) reciprocal best
Mouse  -  Mus musculus             Dec. 2011 (GRCm38/mm10) syntenic
Dog  -  Canis lupus familiaris     Sep. 2011 (Broad CanFam3.1/canFam3) syntenic

Files included in this directory:
  - knownGene.exon*.fa.gz: for each exon in the hg38/GRCh38 Gencode Gene track,
    this file contains either amino acids (AA) or nucleotides (Nuc) for
    hg38/GRCh38 and the aligning genomes.
  - knownCanonical.exon*.fa.gz: for each exon in the hg38/GRCh38 canonical
    set of Gencode Genes, this file contains either amino acids (AA) or
    nucleotides (Nuc) for hg38/GRCh38 and the aligning genomes.
  - refGene.exon*.fa.gz: for each exon in the hg38/GRCh38 RefSeq Gene track,
    this file contains either amino acids (AA) or nucleotides (Nuc) for
    hg38/GRCh38 and the aligning genomes.

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

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To download a large file or multiple files from this directory, we recommend 
that you use ftp rather than downloading the files via our website. To do so: 
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg38/multiz20way/alignments

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.