This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/mm10/phastCons60way/README.txt

This directory contains compressed phastCons scores for multiple alignments
of 59 vertebrate genomes to the mouse genome, plus three alternate sets of
scores for subsets of species in the alignments.

Files in this directory are:

  mm10.60way.phastCons.glire.mod - phastCons tree model for the glire subset:
          mm10 cavPor3 dipOrd1 hetGla2 ochPri2 oryCun2 rn5 speTri2
  mm10.60way.phastCons.euarchontoglire.mod - tree model for the
        euarchontoglire subset: the glire set above, plus:
          tupBel1 calJac3 gorGor3 hg19 micMur1 nomLeu2 otoGar3 panTro4 papHam1
          ponAbe2 rheMac3 saiBol1 tarSyr1
  mm10.60way.phastCons.placental.mod - tree model for the placental subset:
        the glire and euarchontoglire sets above, plus:
          ailMel1 bosTau7 canFam3 choHof1 dasNov3 echTel1 equCab2 eriEur1
          felCat5 loxAfr3 myoLuc2 oviAri1 proCap1 pteVam1 sorAra1 susScr3
          triMan1 turTru2 vicPac1
  mm10.60way.phastCons.mod - phastCons tree model for all 60 species:
        the three subsets above, plus:
          anoCar2 chrPic1 danRer7 fr3 gadMor1 galGal4 gasAcu1 latCha1
          macEug2 melGal1 melUnd1 monDom5 oreNil2 ornAna1 oryLat2 petMar1
          sarHar1 taeGut1 tetNig2 xenTro3

phastCons scores in bigWig format files:
   mm10.60way.phastCons.bw - all 60 species
   mm10.60way.phastCons60wayGlire.bw - glire subset
   mm10.60way.phastCons60wayEuarchontoGlire.bw - euarchontoglire subset
   mm10.60way.phastCons60wayPlacental.bw - placental subset
See also: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
   for bigWig format description

phastCons scores in fixed step wiggle format files:
   mm10.60way.phastCons/*.wigFix.gz - phastCons scores for 60 species
   glire/*.wigFix.gz - phastCons scores for the glire subset
   euarchontoglire/*.wigFix.gz - phastCons scores for the euarchontoglire subset
   placental/*.wigFix.gz - phastCons scores for the placental subset

For a description of the phastCons fixed step wiggle data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html

The phyloP data can be found at:
http://hgdownload.cse.ucsc.edu/goldenPath/mm10/phyloP60way/

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/mm10/multiz60way/

Assemblies used in these alignments:

==== Glire subset:
Mouse           Mus musculus           Dec. 2011  GRCm38/mm10    reference
Guinea pig      Cavia porcellus        Feb. 2008  Broad/cavPor3  Syntenic net
Kangaroo rat    Dipodomys ordii        Jul. 2008  Broad/dipOrd1  Reciprocal best
Naked mole-rat  Heterocephalus glaber  Jan. 2012
                                Broad HetGla_female_1.0/hetGla2  Syntenic net
Pika            Ochotona princeps      Jul. 2008  Broad/ochPri2  Reciprocal best
Rabbit          Oryctolagus cuniculus  Apr. 2009  Broad/oryCun2  Syntenic net
Rat             Rattus norvegicus      Mar. 2012  RGSC 5.0/rn5   Syntenic net
Squirrel        Spermophilus
                     tridecemlineatus  Nov. 2011  Broad/speTri2  Syntenic net

==== Euarchontoglire subset, includes the glire subset above plus:
Tree shrew      Tupaia belangeri       Dec. 2006  Broad/tupBel1  Reciprocal best
Marmoset        Callithrix jacchus     Mar. 2009  WUGSC 3.2/calJac3 Syntenic net
Gorilla         Gorilla gorilla        May. 2011  gorGor3           Syntenic net
Human           Homo sapiens           Feb. 2009  GRCh37/hg19       Syntenic net
Mouse lemur     Microcebus murinus     Jun. 2003  Broad/micMur1  Reciprocal best
Gibbon          Nomascus leucogenys    Jun. 2011  GGSC Nleu1.1/nomLeu2 Syntenic net
Bushbaby        Otolemur garnettii     Mar. 2011  Broad/otoGar3     Syntenic net
Chimp           Pan troglodytes        Feb. 2011
                                 Pan_troglodytes-2.1.4/panTro4      Syntenic net
Baboon          Papio hamadryas        Nov. 2008  Baylor 1.0/papHam1 Reciprocal best
Orangutan       Pongo pygmaeus abelii  July 2007  WUGSC 2.0.2/ponAbe2 Syntenic net
Chinese rhesus  Macaca mulatta         Oct. 2010  BGI CR_1.0/rheMac3 Syntenic net
Squirrel monkey Saimiri boliviensis    Oct. 2011  saiBol1           Syntenic net
Tarsier         Tarsius syrichta       Aug. 2008  Broad/tarSyr1  Reciprocal best

==== Placental subset, includes the glire and euarchontoglire subset above plus:
Panda           Ailuropoda melanoleuca Dec. 2009  BGI-Shenzhen 1.0/ailMel1 Syntenic Net
Cow             Bos taurus             Oct. 2011  Baylor Btau_4.6.1/bosTau7 Syntenic Net
Dog             Canis lupus familiaris Sep. 2011  Broad/canFam3)    Syntenic net
Sloth           Choloepus hoffmanni    Jul. 2008  Broad//choHof1 Reciprocal best
Armadillo       Dasypus novemcinctus   Dec. 2011  Armadillo/dasNov3 Reciprocal best
Tenrec          Echinops telfairi      Jul. 2005  Broad/echTel1  Reciprocal best
Horse           Equus caballus         Sep. 2007  Broad/equCab2  Syntenic net
Hedgehog        Erinaceus europaeus    Jun. 2006  Broad/eriEur1  Reciprocal best
Cat             Felis catus            Sep. 2011
                                          ICGSC Felis_catus 6.2/felCat5 Reciprocal best
Elephant        Loxodonta africana     Jul. 2009  Broad/loxAfr3  Syntenic net
Microbat        Myotis lucifugus       Jul. 2010  Broad/myoLuc2  Reciprocal best
Sheep           Ovis aries             Feb. 2010  ISGC/oviAri1   Reciprocal best
Rock hyrax      Procavia capensis      Jul. 2008  Broad/proCap1  Reciprocal best
Megabat         Pteropus vampyrus      Jul. 2008  Broad/pteVam1  Reciprocal best
Shrew           Sorex araneus          Jun. 2006  Broad/sorAra1  Reciprocal best
Pig             Sus scrofa             Aug. 2011  SGSC Sscrofa10.2/susScr3 Syntenic net
Manatee         Trichechus manatus latirostris Oct. 2011 Broad v1.0/triMan1 Syntenic net
Dolphin         Tursiops truncatus     Oct. 2011  Baylor Ttru_1.4/turTru2 Reciprocal best
Alpaca          Vicugna pacos          Jul. 2008  Broad/vicPac1  Reciprocal best

==== the rest of the vertebrates with the above complete the full 60-way species:
Lizard          Anolis carolinensis    May  2010  Broad/anoCar2         net
Painted turtle  Chrysemys picta bellii Dec. 2011  v3.0.1/chrPic1        net
Zebrafish       Danio rerio            Jul. 2010  Zv9/danRer7           net
Fugu            Takifugu rubripes      Oct. 2011  FUGU5/fr3             net
Atlantic cod    Gadus morhua           May. 2010
                                   Genofisk GadMor_May2010/gadMor1      net
Chicken         Gallus gallus          Nov. 2011
                                   ICGSC Gallus_gallus-4.0/galGal4      net
Stickleback     Gasterosteus aculeatus Feb. 2006  Broad/gasAcu1         net
Coelacanth      Latimeria chalumnae    Aug. 2011  latCha1               net
Wallaby         Macropus eugenii       Sep. 2009  TWGS Meug_1.1/macEug2 Reciprocal best
Turkey          Meleagris gallopavo    Dec. 2009  TGC Turkey_2.01/melGal1 net
Budgerigar      Melopsittacus undulatus Sep. 2011 WUSTL v6.3/melUnd1    net
Opossum         Monodelphis domestica  Oct. 2006  Broad/monDom5         net
Nile tilapia    Oreochromis niloticus  Jan. 2011  Nile tilapia/oreNil2  net
Platypus        Ornithorhynchus anatinus Mar. 2007 WUGSC 5.0.1/ornAna1   net
Medaka          Oryzias latipes        Oct. 2005  NIG/UT MEDAKA1/oryLat2 net
Lamprey         Petromyzon marinus     Mar. 2007  WUGSC 3.0/petMar1     net

Tasmanian devil Sarcophilus harrisii   Feb. 2011
                                   WTSI Devil_ref v7.0/sarHar1          net
Zebra finch     Taeniopygia guttata    Jul. 2008  WUGSC 3.2.4/taeGut1   net
Tetraodon       Tetraodon nigroviridis Mar. 2007  Genoscope 8.0/tetNig2   net
X. tropicalis   Xenopus tropicalis     Nov. 2009  JGI 4.2/xenTro3       net

---------------------------------------------------------------
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 8.5 Gb of compressed data in this directory.

Via rsync:
rsync -avz --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/mm10/phastCons60way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/mm10/phastCons60way

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 available for public use.
For data use restrictions regarding the genome assemblies used in this
annotation, see http://genome.ucsc.edu/goldenPath/credits.html.

---------------------------------------------------------------
References for phastCons and phyloP:

Pollard KS, Hubisz MJ, Siepel A. Detection of non-neutral substitution rates
on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21.
(http://genome.cshlp.org/content/early/2009/10/26/gr.097857.109.abstract)

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson
H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements
in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005
Aug;15(8):1034-50.  (http://www.genome.org/cgi/doi/10.1101/gr.3715005)

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt23-Oct-2012 16:36 9.3K 
[DIR]euarchontoglire/21-Aug-2012 08:55 -  
[DIR]glire/05-Jul-2012 09:08 -  
[TXT]md5sum.txt22-Apr-2014 10:33 544  
[   ]mm10.60way.phastCons.bw17-Apr-2014 16:03 4.3G 
[SND]mm10.60way.phastCons.euarchontoglire.mod16-Apr-2014 10:30 930  
[SND]mm10.60way.phastCons.glire.mod16-Apr-2014 10:27 540  
[SND]mm10.60way.phastCons.mod15-Apr-2014 12:52 2.0K 
[SND]mm10.60way.phastCons.placental.mod16-Apr-2014 10:44 1.5K 
[DIR]mm10.60way.phastCons/05-Jul-2012 09:10 -  
[   ]mm10.60way.phastCons60wayEuarchontoGlire.bw17-Apr-2014 18:13 4.4G 
[   ]mm10.60way.phastCons60wayGlire.bw17-Apr-2014 16:50 4.6G 
[   ]mm10.60way.phastCons60wayPlacental.bw17-Apr-2014 18:30 4.2G 
[DIR]placental/05-Jul-2012 09:08 -  

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