This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phastCons44way/README.txt

This directory contains compressed phastCons scores for multiple
alignments of 44 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 44 species
    primates.mod        phastCons tree model for the primates subset:
	hg18, panTro2, gorGor1, ponAbe2, rheMac2, calJac1, tarSyr1, micMur1,
        otoGar1
	(human, chimp, gorilla, orangutan, rhesus, marmoset, tarsier,
        mouse lemur, bushbaby)
    placentalMammals.mod   phastCons tree model for the placental mammal subset
	hg18, panTro2, gorGor1, ponAbe2, rheMac2, calJac1, tarSyr1, micMur1,
        otoGar1, tupBel1, mm9, rn4, dipOrd1, cavPor3, speTri1, oryCun1, ochPri2
	(human, chimp, gorilla, orangutan, rhesus, marmoset, tarsier,
        mouse lemur, bushbaby, tree shrew, mouse, rat, kangaroo rat,
        guinea pig, ground squirrel, rabbit, pika)

    vertebrate/*.wigFix.gz phastCons scores for 44 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/hg18/multiz44way/

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                   Mar. 2006   hg18
    _ 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
    _ Marmoset        Callithrix jacchus             June 2007   calJac1
    _ Tarsier         Tarsius syrichta               Aug. 2008   tarSyr1
    _ Mouse lemur     Microcebus murinus             Jun. 2003   micMur1
    _ Bushbaby        Otolemur garnettii             Dec. 2006   otoGar1
    _ TreeShrew       Tupaia belangeri               Dec. 2006   tupBel1
    _ Mouse           Mus musculus                   July 2007   mm9
    _ Rat             Rattus norvegicus              Nov. 2004   rn4
    _ Kangaroo rat    Dipodomys ordii                July 2008   dipOrd1
    _ Guinea Pig      Cavia porcellus                Feb. 2008   cavPor3
    _ Squirrel        Spermophilus tridecemlineatus  Feb. 2008   speTri1
    _ Rabbit          Oryctolagus cuniculus          May  2005   oryCun1
    _ Pika            Ochotona princeps              July 2008   ochPri2
    _ Alpaca          Vicugna pacos                  July 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              July 2008   pteVam1
    _ Hedgehog        Erinaceus europaeus            June 2006   eriEur1
    _ Shrew           Sorex araneus                  June 2006   sorAra1
    _ Elephant        Loxodonta africana             July 2008   loxAfr2
    _ Rock hyrax      Procavia capensis              July 2008   proCap1
    _ Tenrec          Echinops telfairi              July 2005   echTel1
    _ Armadillo       Dasypus novemcinctus           July 2008   dasNov2
    _ Sloth           Choloepus hoffmanni            July 2008   choHof1
    _ Opossum         Monodelphis domestica          Jan. 2006   monDom4
    _ Platypus        Ornithorhynchus anatinus       Mar. 2007   ornAna1
    _ Chicken         Gallus gallus                  May  2006   galGal3
    _ Zebra finch     Taeniopygia guttata            July 2008   taeGut1
    _ Lizard          Anolis carolinensis            Feb. 2007   anoCar1
    _ X. tropicalis   Xenopus tropicalis             Aug. 2005   xenTro2
    _ Tetraodon       Tetraodon nigroviridis         Feb. 2004   tetNig1
    _ Fugu            Takifugu rubripes              Oct. 2004   fr2
    _ Stickleback     Gasterosteus aculeatus         Feb. 2006   gasAcu1
    _ Medaka          Oryzias latipes                Oct. 2005   oryLat2
    _ Zebrafish       Danio rerio                    July 2007   danRer5
    _ 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/hg18/phastCons44way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg18/phastCons44way

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:

Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A., Hou, M., 
Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S., 
Weinstock, G.M., Wilson, R. K., Gibbs, R.A., Kent, W.J., Miller, W., 
and Haussler, D.  Evolutionarily conserved elements in vertebrate, insect, 
worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).
(http://www.genome.org/cgi/doi/10.1101/gr.3715005)

Siepel, A. and Haussler, D. Phylogenetic hidden Markov models.
In R. Nielsen, ed., Statistical Methods in Molecular Evolution,
Springer (in press) (2004).
[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[SND]44way.chrX.mod12-Feb-2009 20:04 1.5K 
[TXT]README.txt27-Jan-2009 13:33 6.5K 
[SND]placentalMammals.mod13-Jan-2009 11:21 1.1K 
[DIR]placentalMammals/27-Jan-2009 10:28 -  
[DIR]placentalMammals_v2/22-May-2009 15:13 -  
[SND]primates.mod13-Jan-2009 11:11 534  
[DIR]primates/27-Jan-2009 10:28 -  
[DIR]primates_v2/22-May-2009 15:13 -  
[SND]vertebrate.mod05-Jan-2009 20:46 1.5K 
[DIR]vertebrate/30-Sep-2009 16:27 -  
[DIR]vetebrate_v2/22-May-2009 15:12 -  

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