This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/ce10/multiz7way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the C. elegans genome (ce10, Oct. 2010):

Assemblies used in these alignments:

  - C. elegans                       Oct. 2010  ce10/WS220
  - C. briggsae                      Apr. 2011  cb4/WS225
  - C. remanei                       July 2007  caeRem4/WS220
  - C. sp. 11 ju1373                 Nov. 2010  caeSp111/GCA_000186765.1
  - C. brenneri                      Nov. 2010  caePb3/GCA_000143925.1
  - C. japonica                      Aug. 2010  caeJap4/GCA_000147155.1
  - C. angaria                       Oct. 2010  caeAng1/GCA_000165025.1/WS225

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=ce10&g=cons7way
based on the phylogenetic tree: ce10.7way.nh.

Files in this directory:
  - ce10.7way.nh - phylogenetic tree used during the multiz multiple alignment
  - ce10.commonNames.7way.nh - same as ce10.7way.nh with the UCSC database
	names replaced by the common name for the species
  - ensGene.upstream*.maf.gz - alignments of regions upstream of Ensembl genes
  - chr*.maf.gz - the multiple alignments on C. elegans for each chromosome
  - md5sum.txt - md5 check sums of these files to verify correct download files

The "alignments" directory contains compressed FASTA alignments
for the CDS regions of the C. elegans genome (ce10, Oct. 2010)
aligned to the assemblies.

The chr*.maf.gz files contain all the alignments for the chromosomes
in the C. elegans 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 these
maf files is 198 Mb, uncompressed is more than 420 Mb.

The ensGene.upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for Ensembl genes with annotated 5' UTRs.
These files differ from the standard MAF format: they display
alignments that extend from start to end of the upstream region in 
human, whether or not alignments actually exist. In situations where no  
alignments exist or the alignments of one or more species are missing, 
dot (".") is used as a placeholder. Multiple regions of an assembly's
sequence may align to a single region in C. elegans; therefore, only the 
species name is displayed in the alignment data and no position information 
is recorded. The alignment score is always zero in these files.

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/ce10/phastCons7way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/ce10/phyloP7way

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

Via rsync:
rsync -av --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/ce10/multiz7way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/ce10/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.

---------------------------------------------------------------
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.
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt22-Dec-2011 15:12 4.0K 
[   ]ce10.7way.nh16-Dec-2011 11:02 171  
[   ]ce10.commonNames.7way.nh16-Dec-2011 13:26 200  
[   ]chrI.maf.gz16-Dec-2011 10:18 14M 
[   ]chrII.maf.gz16-Dec-2011 10:18 15M 
[   ]chrIII.maf.gz16-Dec-2011 10:18 14M 
[   ]chrIV.maf.gz16-Dec-2011 10:18 15M 
[   ]chrM.maf.gz16-Dec-2011 10:18 9.3K 
[   ]chrV.maf.gz16-Dec-2011 10:18 19M 
[   ]chrX.maf.gz16-Dec-2011 10:18 24M 
[   ]ensGene.upstream1000.maf.gz16-Dec-2011 13:31 11M 
[   ]ensGene.upstream2000.maf.gz16-Dec-2011 13:32 20M 
[   ]ensGene.upstream5000.maf.gz16-Dec-2011 13:33 64M 
[TXT]md5sum.txt16-Dec-2011 13:34 618  

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