This file is from:

    http://hgdownload.soe.ucsc.edu/goldenPath/mm39/phyloP35way/README.txt

This directory contains conversation scoring by phyloP (phylogenetic p-values)
from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple
alignments of 34 genomes to the mouse mm39/Jun. 2020 genome.


Files in this directory are:

    mm39.phyloP35way.mod  phyloP tree model with branch lengths
                        for all the sequences
    mm39.35way.phyloP/*.wigFix.gz - phyloP scores for all the alignments
                                 in fixed step wiggle format
    mm39.phyloP35way.bw - phyloP scores for all the alignments
                          in bigWig format
    md5sum.txt - md5 sums of the files here to verify accurate download

The multiple alignments and methods description are at:
    http://hgdownload.soe.ucsc.edu/goldenPath/mm39/multiz35way/

For more information about this data, see the track
description for the Conservation track:
    http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm39&g=cons35way

For a description of the phyloP wigFix data file format, see:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
see also the section describing the 'fixedStep' wiggle format:
http://genome.ucsc.edu/goldenPath/help/wiggle.html

Assemblies used in these alignments:

Mouse - Mus musculus
		Jun. 2020 (GRCm39/mm39) (reference)

Beaver - Castor canadensis
		Feb. 2017 (C.can genome v1.0/casCan1) (reciprocal best)
Bonobo - Pan paniscus
		May 2020 (Mhudiblu_PPA_v0/panPan3) (syntenic)
Bushbaby - Otolemur garnettii
		Mar. 2011 (Broad/otoGar3) (reciprocal best)
Chicken - Gallus gallus
		Mar. 2018 (GRCg6a/galGal6) (maf net)
Chimp - Pan troglodytes
		Jan. 2018 (Clint_PTRv2/panTro6) (syntenic)
Chinese hamster - Cricetulus griseus
		Jun. 2020 (GCF_0003668045.3 CriGri-PICRH-1.0) (syntenic)
Chinese pangolin - Manis pentadactyla
		Aug 2014 (M_pentadactyla-1.1.1/manPen1) (reciprocal best)
Cow - Bos taurus
		Apr. 2018 (ARS-UCD1.2/bosTau9) (reciprocal best)
Dog - Canis lupus familiaris
		Mar. 2020 (UU_Cfam_GSD_1.0/canFam4) (syntenic)
Dolphin - Tursiops truncatus
		Oct. 2011 (Baylor Ttru_1.4/turTru2) (reciprocal best)
Elephant - Loxodonta africana
		Jul. 2009 (Broad/loxAfr3) (reciprocal best)
Gorilla - Gorilla gorilla gorilla
		Aug. 2019 (Kamilah_GGO_v0/gorGor6) (syntenic)
Guinea pig - Cavia porcellus
		Feb. 2008 (Broad/cavPor3) (syntenic)
Hawaiian monk seal - Neomonachus schauinslandi
		Jun. 2017 (ASM220157v1/neoSch1) (syntenic)
Hedgehog - Erinaceus europaeus
		May 2012 (EriEur2.0/eriEur2) (reciprocal best)
Horse - Equus caballus
		Jan. 2018 (EquCab3.0/equCab3) (syntenic)
Human - Homo sapiens
		Dec. 2013 (GRCh38/hg38) (syntenic)
Lamprey - Petromyzon marinus
		Dec. 2017 (Pmar_germline 1.0/petMar3) (maf net)
Malayan flying lemur - Galeopterus variegatus
		Jun. 2014 (G_variegatus-3.0.2/galVar1) (maf net)
Marmoset - Callithrix jacchus
		May 2020 (Callithrix_jacchus_cj1700_1.1/calJac4) (syntenic)
Opossum - Monodelphis domestica
		Oct. 2006 (Broad/monDom5) (maf net)
Pig - Sus scrofa
		Aug. 2011 (SGSC Sscrofa10.2/susScr3) (reciprocal best)
Pika - Ochotona princeps
		May 2012 (OchPri3.0/ochPri3) (reciprocal best)
Rabbit - Oryctolagus cuniculus
		Apr. 2009 (Broad/oryCun2) (reciprocal best)
Rat - Rattus norvegicus
		Jul. 2014 (RGSC 6.0/rn6) (syntenic)
Rhesus - Macaca mulatta
		Feb. 2019 (Mmul_10/rheMac10) (syntenic)
Sheep - Ovis aries
		Nov. 2015 (Oar_v4.0/oviAri4) (syntenic)
Shrew - Sorex araneus
		Aug. 2008 (Broad/sorAra2) (reciprocal best)
Squirrel - Spermophilus tridecemlineatus
		Nov. 2011 (Broad/speTri2) (reciprocal best)
Tarsier - Tarsius syrichta
		Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) (reciprocal best)
Tenrec - Echinops telfairi
		Nov. 2012 (Broad/echTel2) (reciprocal best)
Tree shrew - Tupaia belangeri
		Dec. 2006 (Broad/tupBel1) (reciprocal best)
X. tropicalis - Xenopus tropicalis
		Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9) (maf net)
Zebrafish - Danio rerio
		May 2017 (GRCz11/danRer11) (maf net)

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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 9.1 Gb of compressed data in this directory,
approximately 18.6 Gb uncompressed..

Via rsync:
rsync -avz --progress \
	rsync://hgdownload.soe.ucsc.edu/goldenPath/galGal6/phyloP35way/ ./

Via FTP:
    ftp hgdownload.soe.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/galGal6/phyloP35way

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/20/1/110.long)

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://genome.cshlp.org/content/15/8/1034.full)

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      Name                    Last modified      Size  Description
Parent Directory - md5sum.txt 2020-12-23 15:13 109 mm39.35way.phastCons/ 2021-01-27 15:47 - mm39.phyloP35way.bw 2020-12-22 18:52 5.7G mm39.phyloP35way.mod 2020-12-22 13:57 1.3K