This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/README.txt

This directory contains compressed phastCons scores for multiple alignments
of 45 vertebrate genomes to the human genome, plus an alternate set of scores
for the primates subset of species in the alignments, and an alternate set of
scores for the placental mammal subset of species in the alignments.

Files in this directory are:
    vertebrate.mod      phastCons tree model with branch lengths
                        for all 46 species
    primates.mod        phastCons tree model for the primates subset:
	hg19, panTro2, gorGor1, ponAbe2, rheMac2, papHam1, calJac1, tarSyr1,
	micMur1, otoGar1
	(human, chimp, gorilla, orangutan, rhesus, baboon, marmoset, tarsier,
        mouse lemur, bushbaby)
    placentalMammals.mod   phastCons tree model for the placental mammal subset:
	hg19, panTro2, gorGor1, ponAbe2, rheMac2, papHam1, calJac1, tarSyr1, 
	micMur1, otoGar1, tupBel1, mm9, rn4, dipOrd1, cavPor3, speTri1, 
	oryCun2, ochPri2, vicPac1, turTru1, bosTau4, equCab2, felCat3, canFam2, 
	myoLuc1, pteVam1, eriEur1, sorAra1, loxAfr3, proCap1, echTel1, dasNov2, 
	choHof1
	(human, chimp, gorilla, orangutan, rhesus, baboon, marmoset, tarsier,
        mouse lemur, bushbaby, tree shrew, mouse, rat, kangaroo rat,
        guinea pig, ground squirrel, rabbit, pika, alpaca, dolphin, cow,
	horse, cat, dog, microbat, megabat, hedgehog, shrew, elephant,
	rock hyrax, tenrec, armadillo, sloth)

    The models above are calculated only from the chromosomes:
	1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 Y

    vertebrate.chrX.mod	phastCons tree model only for chromosome X
    primates.chrX.mod	phastCons tree model only for chromosome X
    placentalMammals.chrX.mod	phastCons tree model only for chromosome X

    vertebrate/*.wigFix.gz phastCons scores for 46 species
    primates/*.wigFix.gz  phastCons scores for primates subset
    placentalMammals/*.wigFix.gz  phastCons scores for placental mammal subset

The multiple alignments and methods description are at:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/

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

Assemblies used in these alignments:

  - Human         Homo sapiens                  Feb. 2009  hg19/GRCh37
  - Chimp         Pan troglodytes               Mar. 2006  panTro2
  - Gorilla       Gorilla gorilla gorilla       Oct. 2008  gorGor1
  - Orangutan     Pongo pygmaeus abelii         July 2007  ponAbe2
  - Rhesus        Macaca mulatta                Jan. 2006  rheMac2
  - Baboon        Papio hamadryas               Nov. 2008  papHam1
  - Marmoset      Callithrix jacchus            June 2007  calJac1
  - Tarsier       Tarsius syrichta              Aug. 2008  tarSyr1
  - Mouse lemur   Microcebus murinus            Jul. 2007  micMur1
  - Bushbaby      Otolemur garnettii            Dec. 2006  otoGar1
  - Tree shrew    Tupaia belangeri              Dec. 2006  tupBel1
  - Mouse         Mus musculus                  July 2007  mm9   
  - Rat           Rattus norvegicus             Nov. 2004  rn4   
  - Kangaroo rat  Dipodomys ordii               Jul. 2008  dipOrd1
  - Guinea Pig    Cavia porcellus               Feb. 2008  cavPor3
  - Squirrel      Spermophilus tridecemlineatus Feb. 2008  speTri1
  - Rabbit        Oryctolagus cuniculus         Apr. 2009  oryCun2
  - Pika          Ochotona princeps             Jul. 2008  ochPri2
  - Alpaca        Vicugna pacos                 Jul. 2008  vicPac1
  - Dolphin       Tursiops truncatus            Feb. 2008  turTru1
  - Cow           Bos taurus                    Oct. 2007  bosTau4
  - Horse         Equus caballus                Sep. 2007  equCab2
  - Cat           Felis catus                   Mar. 2006  felCat3
  - Dog           Canis lupus familiaris        May  2005  canFam2
  - Microbat      Myotis lucifugus              Mar. 2006  myoLuc1
  - Megabat       Pteropus vampyrus             Jul. 2008  pteVam1
  - Hedgehog      Erinaceus europaeus           June 2006  eriEur1
  - Shrew         Sorex araneus                 June 2006  sorAra1
  - Elephant      Loxodonta africana            Jul. 2009  loxAfr3
  - Rock hyrax    Procavia capensis             Jul. 2008  proCap1
  - Tenrec        Echinops telfairi             July 2005  echTel1
  - Armadillo     Dasypus novemcinctus          Jul. 2008  dasNov2
  - Sloth         Choloepus hoffmanni           Jul. 2008  choHof1
  - Wallaby       Macropus eugenii              Nov. 2007  macEug1
  - Opossum       Monodelphis domestica         Oct. 2006  monDom5
  - Platypus      Ornithorhynchus anatinus      Mar. 2007  ornAna1
  - Chicken       Gallus gallus                 May  2006  galGal3
  - Zebra finch   Taeniopygia guttata           Jul. 2008  taeGut1
  - Lizard        Anolis carolinensis           Feb. 2007  anoCar1
  - X. tropicalis Xenopus tropicalis            Aug. 2005  xenTro2
  - Tetraodon     Tetraodon nigroviridis        Mar. 2007  tetNig2
  - Fugu          Takifugu rubripes             Oct. 2004  fr2   
  - Stickleback   Gasterosteus aculeatus        Feb. 2006  gasAcu1
  - Medaka        Oryzias latipes               Oct. 2005  oryLat2
  - Zebrafish     Danio rerio                   Dec. 2008  danRer6
  - Lamprey       Petromyzon marinus            Mar. 2007  petMar1

---------------------------------------------------------------
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/hg19/phastCons46way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg19/phastCons46way

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. 2009 Oct 26. [Epub ahead of print]
(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.txt08-Oct-2012 09:22 7.0K 
[SND]placentalMammals.chrX.mod10-Nov-2009 13:17 1.2K 
[SND]placentalMammals.mod10-Nov-2009 13:17 1.2K 
[DIR]placentalMammals/30-Oct-2009 09:26 -  
[SND]primates.chrX.mod10-Nov-2009 13:17 564  
[SND]primates.mod10-Nov-2009 13:17 564  
[DIR]primates/01-Dec-2009 11:42 -  
[SND]vertebrate.chrX.mod10-Nov-2009 13:17 1.5K 
[SND]vertebrate.mod10-Nov-2009 13:17 1.5K 
[DIR]vertebrate/30-Oct-2009 09:28 -  

Apache/2.2.15 (CentOS) Server at hgdownload-test.cse.ucsc.edu Port 80