This file is from:

    http://hgdownload.cse.ucsc.edu/goldenPath/mm39/multiz35way/README.txt

This directory contains compressed multiple alignments of
34 genomes to the mouse/mm39/Jun. 2020 genome.

These alignments were prepared using the methods described in the
track description file:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm39&g=cons35way
based on the phylogenetic tree: mm39.35way.nh.

mm39.35way.maf.gz
Files in this directory:
  - mm39.35way.nh - phylogenetic tree used during the multiz multiple
        alignment, using the UCSC database name, or sequence name for those
        sequences that are not hosted in UCSC databases.
  - mm39.35way.scientificName.nh - same as mm39.35way.nh with the
        sequence name replaced with the scientific name for the species.
  - mm39.35way.commonNames.nh - same as mm39.35way.nh with the sequence
        name replaced with the common name
  - mm39.35way.maf.gz - multiple alignments on zebrafish
  - upstream*.ensGene.maf.gz - alignments of regions upstream of
      Ensembl genes
  - 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 the gene track: NCBI RefSeq,
 of the Chinese hamster genome
(GCF_0003668045.3 CriGri-PICRH-1, Jun. 2020) aligned to the assemblies.

The mm39.35way.maf.gz file contains all the alignments on the zebrafish
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 3 Gb, uncompressed is approximately 20 Gb.

The upstream*.ensGene.maf.gz files contain alignments in regions upstream of
annotated transcription starts for Ensembl genes.  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 
chicken, 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 chicken; 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/mm39/phastCons35way

PhyloP conservation scores for these alignments are available at:
http://hgdownload.cse.ucsc.edu/goldenPath/mm39/phyloP35way

---------------------------------------------------------------

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)

---------------------------------------------------------------
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 20 Gb of compressed data in this directory,
approximately 170 Gb uncompressed.

Via rsync:
rsync -av --progress \
	rsync://hgdownload.cse.ucsc.edu/goldenPath/mm39/multiz35way/ ./

Via FTP:
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/mm39/multiz35way

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.
      Name                           Last modified      Size  Description
Parent Directory - upstream5000.ncbiRefSeq.maf.gz 2021-01-04 18:48 1.9G upstream2000.ncbiRefSeq.maf.gz 2021-01-04 17:41 904M upstream300.ncbiRefSeq.maf.gz 2021-01-04 17:04 92M mm39.35way.scientificNames.nh 2020-12-23 15:00 1.6K mm39.35way.nh 2020-12-23 14:56 1.3K mm39.35way.commonNames.nh 2020-12-23 14:59 1.3K md5sum.txt 2021-01-11 15:29 366 maf/ 2021-01-27 15:44 - alignments/ 2021-01-27 15:45 -