This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/ce11/multiz26way/README.txt

This directory contains compressed multiple alignments of the 
following assemblies to the C. elegans genome (ce11, Feb. 2013):

Assemblies used in these alignments:

C. elegans         Caenorhabditis elegans   Feb. 2013 (WBcel235/ce11) reference

A. ceylanicum      Ancylostoma ceylanicum   Mar. 2014
                                         (WS243/Acey_2013.11.30.genDNA/ancCey1)
Barber pole worm   Haemonchus contortus     Jul. 2013  (WormBase WS239/haeCon2)
C. angaria         Caenorhabditis angaria   Mar. 2012           (WS245/caeAng2)
C. brenneri        Caenorhabditis brenneri  Nov. 2010
                                                    (C. brenneri 6.0.1b/caePb3)
C. briggsae        Caenorhabditis briggsae  Apr. 2011               (WS225/cb4)
C. japonica        Caenorhabditis japonica  Aug. 2010     (WUSTL 7.0.1/caeJap4)
C. remanei         Caenorhabditis remanei   Jul. 2007           (WS220/caeRem4)
C. sp. 5 ju800     Caenorhabditis sp5 ju800 Jan. 2012
                                  (WS230/Caenorhabditis_sp_5-JU800-1.0/caeSp51)
C. tropicalis      Caenorhabditis tropicalis Nov. 2010   (WUSTL 3.0.1/caeSp111)
Dog heartworm      Dirofilaria immitis      Sep. 2013
                                                (WS240/D. immitis v2.2/dirImm1)
Eye worm           Loa loa                  Jul. 2012
                                         (WS235/L_loa_Cameroon_isolate/loaLoa1)
Filarial worm      Brugia malayi            May. 2014
                                                   (WS244/B_malayi-3.1/bruMal2)
H. bacteriophora/m31e Heterorhabditis bacteriophora Aug. 2011
                                           (WS229/H. bacteriophora 7.0/hetBac1)
M. hapla           Meloidogyne hapla        Sep. 2008
                                                   (M. hapla VW9 WS210/melHap1)
M. incognita       Meloidogyne incognita    Feb. 2008
                                        (M. incognita WS245/PRJEA28837/melInc2)
Microworm          Panagrellus redivivus    Feb. 2013           (Pred3/panRed1)
N. americanus      Necator americanus       Dec. 2013
                                                (WS242/N_americanus_v1/necAme1)
O. volvulus        Onchocerca volvulus      Nov. 2013
                                         (WS241/O_volvulus_Cameroon_v3/oncVol1)
P. exspectatus     Pristionchus exspectatus Mar. 2014
                                               (WS243/P_exspectatus_v1/priExs1)
P. pacificus       Pristionchus pacificus   Aug. 2014  (P_pacificus-v2/priPac3)
Pig roundworm      Ascaris suum             Sep. 2012
                                                    (WS229/AscSuum_1.0/ascSuu1)
Pine wood nematode Bursaphelenchus xylophilus Nov. 2011 
                                            (WS229/B. xylophilus Ka4C1/burXyl1)
Threadworm         Strongyloides ratti      Sep. 2014  (S. ratti ED321/strRat2)
Trichinella        Trichinella spiralis     Jan. 2011
                                     (WS225/Trichinella_spiralis-3.7.1/triSpi1)
Whipworm           Trichuris suis           Jul. 2014 (WS243/T. suis
                                                       DCEP-RM93M male/triSui1)

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=ce11&g=cons26way
based on the phylogenetic tree: ce11.26way.nh.

Files in this directory:
  - ce11.26way.nh - phylogenetic tree used during the multiz multiple alignment
  - ce11.26way.commonNames.nh - same as ce11.26way.nh with the UCSC database
	names replaced by the common name for the species
  - ce11.26way.scientificName.nh - same as ce11.26way.nh with the UCSC database
	names replaced by the scientific name for the species
  - upstream*.ensGene..maf.gz - alignments of regions upstream of Ensembl genes
  - upstream*.refGene..maf.gz - alignments of regions upstream of RefSeq genes
  - upstream*.ws245Genes..maf.gz - alignments of regions upstream of ws245 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 for three gene tracks, ws245Genes, refGene, ensGene,
 of the C. elegans genome (ce11, Feb. 2013) 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 33 Mb, uncompressed is more than 2.4 Gb.

The .upstream*.*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for Ensembl genes, RefSeq genes, and
the WormBase WS245 gene predictions, 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 
C. elegans, 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/ce11/phastCons26way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/ce11/phyloP26way

---------------------------------------------------------------
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/ce11/multiz26way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/ce11/multiz26way

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.txt23-Mar-2016 12:53 6.8K 
[DIR]alignments/09-Sep-2015 11:30 -  
[   ]ce11.26way.commonNames.nh08-Sep-2015 14:15 968  
[   ]ce11.26way.nh08-Sep-2015 14:15 869  
[   ]ce11.26way.scientificNames.nh08-Sep-2015 14:15 1.2K 
[   ]chrI.maf.gz13-Aug-2015 14:42 54M 
[   ]chrII.maf.gz13-Aug-2015 14:42 51M 
[   ]chrIII.maf.gz13-Aug-2015 14:42 51M 
[   ]chrIV.maf.gz13-Aug-2015 14:42 56M 
[   ]chrM.maf.gz13-Aug-2015 14:41 137K 
[   ]chrV.maf.gz13-Aug-2015 14:42 63M 
[   ]chrX.maf.gz13-Aug-2015 14:42 58M 
[TXT]md5sum.txt09-Sep-2015 12:35 1.0K 
[   ]upstream1000.ensGene.maf.gz09-Sep-2015 11:50 36M 
[   ]upstream1000.refGene.maf.gz09-Sep-2015 10:51 84M 
[   ]upstream1000.ws245Genes.maf.gz08-Sep-2015 17:03 35M 
[   ]upstream2000.ensGene.maf.gz09-Sep-2015 11:54 77M 
[   ]upstream2000.refGene.maf.gz09-Sep-2015 11:15 193M 
[   ]upstream2000.ws245Genes.maf.gz08-Sep-2015 17:07 77M 
[   ]upstream5000.ensGene.maf.gz09-Sep-2015 12:00 188M 
[   ]upstream5000.refGene.maf.gz09-Sep-2015 11:34 471M 
[   ]upstream5000.ws245Genes.maf.gz08-Sep-2015 17:13 188M 

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