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: go to the directory goldenPath/mm39/multiz35way To download multiple files from the UNIX command line, use the "mget" command. mget ... - 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.