This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/xenTro9/multiz11way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the X. tropicalis genome (xenTro9, Jul. 2016):

Assemblies used in these alignments:

- X. tropicalis       Xenopus tropicalis     Jul. 2016  DOE JGI v9.1/xenTro9
                                                        reference genome

- African clawed frog Xenopus laevis         Aug. 2016  IXSC v2/xenLae2
- Tibetan frog        Nanorana parkeri       Mar. 2015  BGI ZX_2015/nanPar1
- Painted turtle      Chrysemys picta bellii Mar. 2014  IPTGSC v3.0.3/chrPic2
- Chicken             Gallus gallus          May  2006  Gallus_gallus-5.0/galGal5
- Lizard              Anolis carolinensis    May  2010  anoCar2/Broad
- Opossum             Monodelphis domestica  Oct. 2006  Broad/monDom5
- Dog                 Canis lupus familiaris Sep. 2011  Broad CanFam3.1/canFam3
- Human               Homo sapiens           Dec. 2013  GRCh38/hg38
- Mouse               Mus musculus           Dec. 2011  GRCm38/mm10
- Fugu                Takifugu rubripes      Oct. 2011  FUGU5/fr3

Syntenic net filtered MAF files used for multiz:
   hg38, mm10, xenLae2, canFam3, monDom5, fr3, galGal5, anoCar2
Reciprocal best filtered MAF files used for multiz:
   nanPar1 chrPic2

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=xenTro9&g=cons11way
based on the phylogenetic tree: xenTro9.11way.nh.

Files in this directory:
 - xenTro9.11way.nh - phylogenetic tree used during the multiz multiple alignment
 - xenTro9.11way.commonNames.nh - same as xenTro9.11way.nh with the UCSC database
	names replaced by the common name for the species
 - xenTro9.11way.scientificName.nh - same as xenTro9.11way.nh with the UCSC
	database names replaced by the scientific name for the species
 - xenTro9.11way.maf.gz - the multiple alignments on the
        X. tropicalis reference genome
 - upstream*.refGene.maf.gz - alignments of regions upstream of refGene genes
 - md5sum.txt - md5 check sums of these files to verify correct download files

The xenTro9.11way.maf.gz file contain all the alignments for the chromosomes
in the X. tropicalis genome, including additional annotations to
indicate gap context and genomic breaks for the sequence in the underlying
genome assemblies.  Note, the compressed data size of the
maf file is 853 Mb, uncompressed is 4.0 Gb.

The "alignments" directory contains compressed FASTA alignments
for the CDS regions of the Xenopus genome (xenTro9, Jul. 2016)
aligned to the assemblies.

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=xenTro9&g=cons11way
based on the phylogenetic tree: xenTro9.11way.nh.

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

PhastCons conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/xenTro9/phastCons11way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/xenTro9/phyloP11way

---------------------------------------------------------------
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 934 Mb of compressed data in this directory.

Via rsync:
rsync -av --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro9/multiz11way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/xenTro9/multiz11way

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/ 2017-05-02 16:48 - md5sum.txt 2017-05-02 14:50 422 upstream1000.refGene.maf.gz 2017-05-02 14:38 5.3M upstream2000.refGene.maf.gz 2017-05-02 14:39 8.8M upstream5000.refGene.maf.gz 2017-05-02 14:40 21M xenTro9.11way.commonNames.nh 2017-05-02 14:49 326 xenTro9.11way.maf.gz 2017-05-02 10:33 853M xenTro9.11way.nh 2017-05-02 14:48 301 xenTro9.11way.scientificNames.nh 2017-05-02 14:49 418