ftp://ftp.ccb.jhu.edu/pub/software/phylocsfpp/hub.txt PhyloCSF++ Evolutionary protein-coding potential as measured by PhyloCSF++ 2021-03-16 15:33:32 5 rn6,fr3,gasAcu1,tarSyr2,sacCer3, ftp://ftp.ccb.jhu.edu/pub/software/phylocsfpp/hub.html
ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/genome_browser_hub/hub.txt rfam12_ncRNA Rfam 12.0 non-coding RNA annotation 2015-05-06 11:32:56 8 hg38,mm10,ce10,galGal4,ci2,danRer7,dm6,sacCer3, ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/genome_browser_hub/ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/genome_browser_hub/hub_description.html
http://augustus.uni-greifswald.de/hubs/argiope/hub.txt Wasp spider hub This is the assembly hub of the wasp spider (Argiope bruennichi) 2020-08-26 07:08:09 1 argiope, http://augustus.uni-greifswald.de/hubs/argiope/aboutHub.html
http://augustus.uni-greifswald.de/hubs/pisaster/hub.txt Purple sea star Assembly Hub This is the Assembly Hub of the purple sea star (Pisaster ochraceus, assembly 12Jun2017_28pcJ) 2019-04-15 11:07:43 1 12Jun2017_28pcJ, http://augustus.uni-greifswald.de/hubs/pisaster/aboutHub.html
http://bx.psu.edu/~yuzhang/Roadmap_ideas/ideas_hub.txt IDEAS roadmap 20states Roadmap Epigenomics 20 state genome segmentation using the IDEAS algorithm 2017-10-04 14:19:48 1 hg19, https://academic.oup.com/nar/article/45/17/9823/4056234/Accurate-and-reproducible-functional-maps-in-127
http://cotneylab.cam.uchc.edu/~jcotney/HEART_HUB/heart_hub.txt Cotney Lab Human Embryonic Heart Hub Human Embryonic Heart Tissue Epigenomic and Transcriptomic Data from the Cotney Lab at UConn Health 2020-03-18 11:58:57 2 hg19,hg38, http://cotney.research.uchc.edu
http://dbrip.org/dbRIPHub/hub.txt dbRIP_Hub "dbRIP: Database of Polymorphic and Species-specific Retrotransposons in Humans" 2018-05-04 10:40:26 2 hg19,hg38, http://dbrip.org/dbRIPHub/dbRIP_Hub.html
http://epigenomesportal.ca/hub/hub.txt McGill EMC (CEEHRC) McGill Epigenomics Mapping Centre, Montreal, Quebec, Canada 2013-12-09 16:46:28 1 hg19, NULL
http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt JASPAR TFBS TFBS predictions for profiles in the JASPAR CORE collections 2017-09-27 09:59:05 12 hg19,hg38,ce10,ce11,ci3,dm6,sacCer3,danRer10,danRer11,mm10,mm39,araTha1, http://jaspar.genereg.net/genome-tracks/
http://fantom.gsc.riken.jp/5/datahub/hub.txt FANTOM5 RIKEN FANTOM5 Phase1 and Phase2 data 2014-08-11 16:10:40 8 hg38,mm10,hg19,mm9,canFam3,rn6,rheMac8,galGal5, https://fantom.gsc.riken.jp/5/datahub/description.html
http://fantom.gsc.riken.jp/5/suppl/Ohmiya_et_al_2014/data/hub.txt FANTOM5 CAGE RECLU DATA RIKEN FANTOM5 CAGE clusters by RECLU 2014-09-09 10:58:04 2 hg19,hg18, http://fantom.gsc.riken.jp/5/suppl/Ohmiya_et_al_2014/
http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/current_release/homo_sapiens/hub/hub.txt Blueprint Hub Blueprint Epigenomics Data Hub 2013-07-23 11:43:54 1 hg38, http://www.blueprint-epigenome.eu/index.cfm?p=31AD6D30-9B3C-BB97-E7F81875121FEC41
http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt ENCODE Analysis Hub ENCODE Integrative Analysis Data Hub 2012-09-04 12:24:47 1 hg19, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439153/
http://ftp.ebi.ac.uk/pub/databases/gencode/covid19_trackhub/hub.txt COVID-19 Gene Annotation GENCODE annotation of COVID-19 associated genes 2020-05-29 14:52:43 1 hg38, http://ftp.ebi.ac.uk/pub/databases/gencode/covid19_trackhub/COVID19_Hub.html
http://ftp.ebi.ac.uk/pub/databases/gencode/update_trackhub/hub.txt GENCODE Annotation Updates Updates to GENCODE manual annotation since last release 2020-09-23 16:32:58 3 hg38,mm39,mm10, http://ftp.ebi.ac.uk/pub/databases/gencode/update_trackhub/GENCODE_Updates.html
http://ftp.ensembl.org/pub/papers/regulation/hub.txt Ensembl Regulatory Build Evidence summaries and provisional results for the new Ensembl Regulatory Build 2014-09-22 13:18:24 3 hg38,hg19,mm10, http://ensembl.org/info/genome/funcgen/regulatory_build.html
http://gengastro.med.tu-dresden.de/suppl/footprint/Hub/tisHub.txt Translation Initiation Sites (TIS) Translation Initiation Sites (TIS) track 2013-04-03 10:14:16 1 hg19, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483550/
http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt Ultraconserved Elements Ultra conserved Elements in the Human Genome. Science 304(5675) pp.1321-1325 (2004) 2014-01-23 16:10:02 1 hg19, http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/ultraConserved.html
http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt GTEx RNA-seq Signal Hub RNA-seq read coverage in 53 tissues from GTEx V6 (7572 samples) 2016-06-01 17:47:11 2 hg19,hg38, http://hgdownload.soe.ucsc.edu/hubs/gtex/gtexHub.html
http://hgdownload.soe.ucsc.edu/hubs/gtexAnalysis/hub.txt GTEx Analysis Hub Genotype Tissue Expression (GTEx) Project Analysis Hub 2016-08-29 13:48:38 2 hg19,hg38, http://hgdownload.soe.ucsc.edu/hubs/gtexAnalysis/gtexAnalysisHub.html
http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt Mouse strain assemblies Assembly and alignment data for 16 different mouse strains plus rat. 2017-06-30 14:08:24 18 mm10,rn6,129S1_SvImJ,WSB_EiJ,SPRET_EiJ,AKR_J,DBA_2J,CBA_J,A_J,C57BL_6NJ,CAST_EiJ,PWK_PhJ,LP_J,C3H_HeJ,NZO_HlLtJ,NOD_ShiLtJ,FVB_NJ,BALB_cJ, http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hubIndex.html
http://hgdownload.soe.ucsc.edu/hubs/neuroDiffCrispr/hubNeuroDiffCrispr.txt Primate x4 NeuroDiff and Human CRISPRa RNAseq coverage tracks from 4 Primate neuro-differentiation assays and a human CRISPRa assay 2018-12-19 16:32:17 4 hg19,panTro4,ponAbe2,rheMac8, http://hgdownload.soe.ucsc.edu/hubs/neuroDiffCrispr/hubNeuroDiffCrispr.html
http://innovebioinfo.com/Annotation/Polytracts/trackHub/hub.txt Polytract Repeats Very Short Tandem Repeats (MNR/DNR/TNR) 2020-02-21 16:20:05 4 hg38,mm10,rn6,dm6, http://innovebioinfo.com/Annotation/Polytracts/Polytract.html
http://lasallelab.genomecenter.ucdavis.edu/UCSChub/hub.txt UCD Methylation UCD DNA methylation data 2015-08-07 12:17:53 11 hg19,hg18,mm10,mm9,bosTau7,bosTau6,canFam3,equCab2,monDom5,rheMac2,rheMac3, NULL
http://lisanwanglab.org/DASHR/tracks/hub.txt DASHR small ncRNA Hub DASHR Human small non-coding RNA data 2015-12-20 11:30:47 1 hg19, http://lisanwanglab.org/DASHR/
http://ngs.sanger.ac.uk/production/grit/track_hub/hub.txt GRC Genome Issues under Review Genome Reference Consortium: Genome issues and other features 2015-04-02 11:45:33 7 hg38,hg19,mm10,mm9,danRer7,danRer10,danRer11, http://www.ncbi.nlm.nih.gov/pubmed/21750661
http://portal.nersc.gov/dna/RD/ChIP-Seq/VISTA_enhancer_e/VistaEnhancerTrackHub/hub.txt Vista Enhancers Vista Browser Track Hub 2015-07-29 12:30:05 3 hg19,mm9,mm10, http://enhancer.lbl.gov
http://raw.githubusercontent.com/mhalushka/miRNA-UCSC-hub/master/hub.txt Human cellular microRNAome microRNA RNA-seq based data from 46 primary cell types and 42 cancer or immortalized cell lines. 2017-06-02 14:11:29 1 hg38, http://biorxiv.org/content/early/2017/03/24/120394
http://reftss.clst.riken.jp/trackhub/hub.txt refTSS refTSS 2020-03-06 14:05:02 2 hg38,mm10,
http://remap.univ-amu.fr/storage/public/hubReMap2018/hub.txt ReMap 2018 Regulatory Atlas ReMap 2018: An atlas of regulatory regions from an integrative analysis of Human DNA-binding sequencing experiments. Go to ReMap for more info. Pubmed link. 2017-10-06 13:11:33 1 hg38, http://remap.univ-amu.fr/storage/public/hubReMap2018/remapHub.html
http://remap.univ-amu.fr/storage/public/hubReMap2020UCSC/hub.txt ReMap 2020 Regulatory Atlas ReMap 2020: An atlas of regulatory regions from an integrative analysis of Human and Arabidopsis thaliana DNA-binding sequencing experiments. Go to ReMap for more info. 2019-09-18 13:32:09 2 hg38,araTha1, http://remap.univ-amu.fr/storage/public/hubReMap2020UCSC/remapHub2020.html
http://research.nhgri.nih.gov/manuscripts/Burgess/zebrafish/downloads/NHGRI-1/hub.txt ZebrafishGenomics Burgess Lab Zebrafish Genomic Resources 2017-02-03 13:31:58 3 danRer11,danRer10,danRer7, https://research.nhgri.nih.gov/manuscripts/Burgess/zebrafish/download.shtml
http://siomilab.sakura.ne.jp/external/hamster_ucsc_browser/hub.txt Golden Hamster genome Genome assembly of Golden Hamster(Mesocricetus auratus) from Siomi lab 2021-12-07 13:48:18 1 MesAur2.0, http://siomilab.sakura.ne.jp/external/hamster_ucsc_browser/MesAur2.0/docs/description.html
http://smithlab.usc.edu/trackdata/methylation/hub.txt MethBase2 Thousands of analyzed methylomes / DNA methylation profiles from bisulfite sequencing data 2024-08-26 14:47:53 13 hg38,apiMel2,bosTau9,canFam6,danRer11,galGal6,gorGor6,mm39,oviAri4,panTro6,rheMac10,rn7,susScr11, https://github.com/smithlabcode/methbase
http://trackhub.genereg.net/promoterome/hub.txt Promoterome CAGE and nucleosome positioning Zebrafish promoterome based on Haberle et al. and Nepal et al. 2016-03-18 14:14:03 1 danRer7, http://trackhub.genereg.net/promoterome/danRer7/index.html
http://waterston.gs.washington.edu/trackhubs/isolates/hub.txt C_elegans_isolates C. elegans wild isolate assembly hub 2015-05-19 10:09:19 3 CB4856Princeton_JR-contig,CB4856Princeton_cycle20,CB4856Princeton_Contigs, http://www.ncbi.nlm.nih.gov/pubmed/25995208
http://www.3402bioinformaticsgroup.com/wp-content/uploads/2016/07/ucsc_track_hub/hub.txt Xmac Xiphophorus maculatus chromosome assembly version 5.0(SMRT) 2019-10-24 12:23:36 1 X.maculatus, http://www.3402bioinformaticsgroup.com/wp-content/uploads/2016/07/ucsc_track_hub/X.maculatus/description.html
http://www.bcgsc.ca/downloads/edcc/data/CEMT/hub/bcgsc_datahub.txt CEMT (CEEHRC) Epigenomic Data tracks from BCGSC, Vancouver, B.C. 2013-09-13 16:28:04 2 hg38,hg19, http://www.epigenomes.ca
http://www.bioinf.uni-leipzig.de/Publications/SUPPLEMENTS/20-002/SIHUMI_track_hub/hub.txt SIHUMI simplified human intestinal microbiota HUB 2021-08-11 10:07:17 8 bact,bifi,blautia,anaero,ery,clostri,lacto,ecoli, https://pubmed.ncbi.nlm.nih.gov/34039272/
http://www.imperial.ac.uk/medicine/beta-cell-genome-regulation-laboratory/data/HILNCs/HILNCs.txt Human Islet lncRNAs Pancreatic islet long non coding RNA transcripts (Akerman et al 2016) 2016-10-17 11:02:15 1 hg19, https://www.imperial.ac.uk/medicine//beta-cell-genome-regulation-laboratory/data/HILNCs/hg19/HILNCs.html
http://www.informatics.jax.org/downloads/TrackHubs/hub.txt MGI Alleles and Phenotypes Allele's and Phenotypes from the Mouse Genome Informatics (MGI) consortium 2017-10-20 15:11:20 1 mm10, http://www.informatics.jax.org/downloads/TrackHubs/description.html
http://www.mircode.org/ucscHub/hub.txt miRcode microRNA sites Predicted microRNA target sites in GENCODE transcripts 2012-09-18 10:18:03 1 hg19, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400968/
http://wyngb.gladstone.org/data/swhalen/pec_mpra/hub.txt PsychENCODE MPRA Hub PsychENCODE MPRA Hub 2023-04-10 15:12:25 1 hg38, https://doi.org/10.1101/2023.02.15.528663
http://younglab.wi.mit.edu/mESC_ChIAPET_hub/hub.txt mm9.SMC1.ChIAPET Cohesin(Smc1)-associated chromatin interactions in murine embryonic stem cells 2015-11-04 08:07:36 1 mm9, http://younglab.wi.mit.edu/mESC_ChIAPET_hub/description.html
http://zlab-trackhub.umassmed.edu/shulhah/hub.txt UMassMed ZHub UMassMed H3K4me3 ChIP-seq data for Autistic brains 2012-03-02 14:14:27 1 hg19, http://archpsyc.jamanetwork.com/article.aspx?articleid=1107452
https://apprisws.bioinfo.cnio.es/trackHub/hub.txt Principal Splice Isoforms APPRIS Selects a single CDS variant for each gene as the 'PRINCIPAL' isoform based on the range of protein features. 2016-02-25 09:24:05 9 hg38,hg19,mm10,danRer10,rn6,susScr3,panTro4,dm6,ce10, https://apprisws.bioinfo.cnio.es/trackHub/docs/trackHub
https://apprisws.bioinfo.cnio.es/trackHubPROTEO/hub.txt Peptide evidences CNIO Peptides detected from a re-analysis of multiple experiments and databases 2016-02-05 08:22:02 2 hg38,hg19, https://apprisws.bioinfo.cnio.es/trackHubPROTEO/docs/PROTEO.html
https://bchub.epfl.ch/breastca.txt Breast Cancer Epigenomics Track Hub Breast Cancer Epigenomics Track Hub 2022-11-18 15:39:38 1 hg19, https://bchub.epfl.ch
https://bds.mpi-cbg.de/hillerlab/CESAR/trackHub/hub.txt CESAR Gene Mappings Human Exons mapped by CESAR 2016-04-24 13:04:53 99 bosTau7,ailMel1,allMis1,anoCar2,calJac3,canFam3,cavPor3,cerSim1,chrPic1,criGri1,danRer7,dasNov3,echTel2,equCab2,eriEur2,felCat5,fr3,gadMor1,galGal4,gasAcu1,geoFor1,gorGor3,hetGla2,latCha1,loxAfr3,macEug2,macFas5,melGal1,melUnd1,mm10,monDom5,musFur1,myoLuc2,nomLeu3,ochPri3,oreNil2,ornAna1,oryCun2,oryLat2,otoGar3,oviAri3,panTro4,papHam1,petMar2,ponAbe2,pteVam1,rheMac3,rn5,saiBol1,sarHar1,sorAra2,speTri2,susScr3,taeGut2,tetNig2,triMan1,turTru2,vicPac2,xenTro7,hub.amaVit1,hub.anaPla1,hub.apaSpi1,hub.araMac1,hub.astMex1,hub.camFer1,hub.capHir1,hub.cheMyd1,hub.chiLan1,hub.chlSab1,hub.chrAsi1,hub.colLiv1,hub.conCri1,hub.eleEdw1,hub.eptFus1,hub.falChe1,hub.falPer1,hub.ficAlb2,hub.hapBur1,hub.jacJac1,hub.lepOcu1,hub.lepWed1,hub.mayZeb1,hub.mesAur1,hub.micOch1,hub.myoDav1,hub.neoBri1,hub.octDeg1,hub.odoRosDiv1,hub.orcOrc1,hub.oryAfe1,hub.panHod1,hub.pelSin1,hub.pseHum1,hub.pteAle1,hub.punNye1,hub.takFla1,hub.tupChi1,hub.xipMac1,hub.zonAlb1, https://bds.mpi-cbg.de/hillerlab/CESAR/trackHub/CESAR.html
https://bioinf.uni-greifswald.de/hubs/sunflower_sea_star/hub.txt sunflower_sea_star Pycnopodia helianthoides (sunflower sea star) 2023-07-17 14:41:24 1 sunflower_sea_star, https://bioinf.uni-greifswald.de/hubs/sunflower_sea_star/description.html
https://brcaexchange.org/trackhubs/hub.txt BRCAExchange BRCAExchange annotated BRCA1/2 variants 2024-08-27 14:59:51 2 hg19,hg38, https://www.brcaexchange.org/trackhubs/description.html
https://cdn.genecards.org/hubs/genecarna/hub.txt GeneCards ncRNAs An integrated compendium of ncRNA genes in GeneCards 2021-05-03 11:06:39 1 hg38, http://www.genecards.org/Guide/GeneCard/transcripts
https://cdn.genecards.org/hubs/genehancer/hub.txt GeneHancer GeneHancer: genome-wide integration of regulatory elements and target genes in GeneCards 2017-04-07 12:50:33 2 hg38,hg19, http://www.genecards.org/Guide/GeneCard/enhancers
https://cgl.gi.ucsc.edu/data/cactus/363-avian-2020-hub/hub.txt Bird Alignment (363 species) Bird Alignment (363 species) 2022-01-18 16:21:24 363 Gallus_gallus,Acanthisitta_chloris,Acrocephalus_arundinaceus,Aegithalos_caudatus,Aegotheles_bennettii,Agapornis_roseicollis,Agelaius_phoeniceus,Alaudala_cheleensis,Alca_torda,Aleadryas_rufinucha,Alectura_lathami,Alopecoenas_beccarii,Amazona_guildingii,Anas_platyrhynchos,Anas_zonorhyncha,Anhinga_anhinga,Anhinga_rufa,Anser_cygnoid,Anseranas_semipalmata,Anthoscopus_minutus,Antrostomus_carolinensis,Apaloderma_vittatum,Aphelocoma_coerulescens,Aptenodytes_forsteri,Apteryx_australis,Apteryx_haastii,Apteryx_owenii,Apteryx_rowi,Aquila_chrysaetos,Aramus_guarauna,Ardeotis_kori,Arenaria_interpres,Asarcornis_scutulata,Atlantisia_rogersi,Atrichornis_clamosus,Balaeniceps_rex,Balearica_regulorum,Baryphthengus_martii,Bombycilla_garrulus,Brachypodius_atriceps,Brachypteracias_leptosomus,Bucco_capensis,Buceros_rhinoceros,Bucorvus_abyssinicus,Buphagus_erythrorhynchus,Burhinus_bistriatus,Cairina_moschata,Calcarius_ornatus,Calidris_pugnax,Callaeas_wilsoni,Callipepla_squamata,Caloenas_nicobarica,Calonectris_borealis,Calypte_anna,Calyptomena_viridis,Campylorhamphus_procurvoides,Cardinalis_cardinalis,Cariama_cristata,Casuarius_casuarius,Cathartes_aura,Catharus_fuscescens,Centropus_bengalensis,Centropus_unirufus,Cephalopterus_ornatus,Cepphus_grylle,Cercotrichas_coryphaeus,Certhia_brachydactyla,Certhia_familiaris,Cettia_cetti,Ceuthmochares_aereus,Ceyx_cyanopectus,Chaetops_frenatus,Chaetorhynchus_papuensis,Chaetura_pelagica,Charadrius_alexandrinus,Charadrius_vociferus,Chauna_torquata,Chionis_minor,Chlamydotis_macqueenii,Chloroceryle_aenea,Chlorodrepanis_virens,Chloropsis_cyanopogon,Chloropsis_hardwickii,Chordeiles_acutipennis,Chroicocephalus_maculipennis,Chunga_burmeisteri,Ciccaba_nigrolineata,Ciconia_maguari,Cinclus_mexicanus,Circaetus_pectoralis,Cisticola_juncidis,Climacteris_rufus,Cnemophilus_loriae,Cochlearius_cochlearius,Colinus_virginianus,Colius_striatus,Columba_livia,Columbina_picui,Copsychus_sechellarum,Corvus_brachyrhynchos,Corvus_cornix,Corvus_moneduloides,Corythaeola_cristata,Corythaixoides_concolor,Coturnix_japonica,Crotophaga_sulcirostris,Crypturellus_cinnamomeus,Crypturellus_soui,Crypturellus_undulatus,Cuculus_canorus,Daphoenositta_chrysoptera,Dasyornis_broadbenti,Dicaeum_eximium,Dicrurus_megarhynchus,Donacobius_atricapilla,Dromaius_novaehollandiae,Dromas_ardeola,Drymodes_brunneopygia,Dryoscopus_gambensis,Dyaphorophyia_castanea,Edolisoma_coerulescens,Egretta_garzetta,Elachura_formosa,Emberiza_fucata,Eolophus_roseicapillus,Erithacus_rubecula,Erpornis_zantholeuca,Erythrocercus_mccallii,Eubucco_bourcierii,Eudromia_elegans,Eulacestoma_nigropectus,Eurypyga_helias,Eurystomus_gularis,Falco_cherrug,Falco_peregrinus,Falcunculus_frontatus,Ficedula_albicollis,Formicarius_rufipectus,Fregata_magnificens,Fregetta_grallaria,Fulmarus_glacialis,Furnarius_figulus,Galbula_dea,Gavia_stellata,Geococcyx_californianus,Geospiza_fortis,Glareola_pratincola,Glaucidium_brasilianum,Grallaria_varia,Grantiella_picta,Grus_americana,Gymnorhina_tibicen,Halcyon_senegalensis,Haliaeetus_albicilla,Haliaeetus_leucocephalus,Heliornis_fulica,Hemignathus_wilsoni,Hemiprocne_comata,Herpetotheres_cachinnans,Himantopus_himantopus,Hippolais_icterina,Hirundo_rustica,Horornis_vulcanius,Hydrobates_tethys,Hylia_prasina,Hypocryptadius_cinnamomeus,Ibidorhyncha_struthersii,Ifrita_kowaldi,Illadopsis_cleaveri,Indicator_maculatus,Irena_cyanogastra,Jacana_jacana,Junco_hyemalis,Lanius_ludovicianus,Larus_smithsonianus,Leiothrix_lutea,Lepidothrix_coronata,Leptocoma_aspasia,Leptosomus_discolor,Leucopsar_rothschildi,Limosa_lapponica,Locustella_ochotensis,Lonchura_striata,Lophotis_ruficrista,Loxia_curvirostra,Loxia_leucoptera,Machaerirhynchus_nigripectus,Malurus_elegans,Manacus_manacus,Melanocharis_versteri,Meleagris_gallopavo,Melopsittacus_undulatus,Melospiza_melodia,Menura_novaehollandiae,Merops_nubicus,Mesembrinibis_cayennensis,Mesitornis_unicolor,Mionectes_macconnelli,Mohoua_ochrocephala,Molothrus_ater,Motacilla_alba,Myiagra_hebetior,Mystacornis_crossleyi,Neodrepanis_coruscans,Neopipo_cinnamomea,Nesospiza_acunhae,Nestor_notabilis,Nicator_chloris,Nipponia_nippon,Nothocercus_julius,Nothocercus_nigrocapillus,Nothoprocta_ornata,Nothoprocta_pentlandii,Nothoprocta_perdicaria,Notiomystis_cincta,Numida_meleagris,Nyctibius_bracteatus,Nyctibius_grandis,Nycticryphes_semicollaris,Nyctiprogne_leucopyga,Oceanites_oceanicus,Odontophorus_gujanensis,Oenanthe_oenanthe,Onychorhynchus_coronatus,Opisthocomus_hoazin,Oreocharis_arfaki,Oreotrochilus_melanogaster,Origma_solitaria,Oriolus_oriolus,Orthonyx_spaldingii,Oxylabes_madagascariensis,Oxyruncus_cristatus,Pachycephala_philippinensis,Pachyramphus_minor,Pandion_haliaetus,Panurus_biarmicus,Paradisaea_raggiana,Pardalotus_punctatus,Parus_major,Passer_domesticus,Passerina_amoena,Patagioenas_fasciata,Pedionomus_torquatus,Pelecanoides_urinatrix,Pelecanus_crispus,Penelope_pileata,Peucedramus_taeniatus,Phaethon_lepturus,Phaetusa_simplex,Phainopepla_nitens,Phalacrocorax_auritus,Phalacrocorax_brasilianus,Phalacrocorax_carbo,Phalacrocorax_harrisi,Phalacrocorax_pelagicus,Phasianus_colchicus,Pheucticus_melanocephalus,Phoenicopterus_ruber,Phylloscopus_trochilus,Piaya_cayana,Picathartes_gymnocephalus,Picoides_pubescens,Piprites_chloris,Pitta_sordida,Ploceus_nigricollis,Pluvianellus_socialis,Podargus_strigoides,Podiceps_cristatus,Podilymbus_podiceps,Poecile_atricapillus,Polioptila_caerulea,Pomatorhinus_ruficollis,Pomatostomus_ruficeps,Probosciger_aterrimus,Promerops_cafer,Prunella_fulvescens,Prunella_himalayana,Pseudopodoces_humilis,Psilopogon_haemacephalus,Psophia_crepitans,Pterocles_burchelli,Pterocles_gutturalis,Pteruthius_melanotis,Ptilonorhynchus_violaceus,Ptilorrhoa_leucosticta,Pycnonotus_jocosus,Pygoscelis_adeliae,Quiscalus_mexicanus,Ramphastos_sulfuratus,Regulus_satrapa,Rhabdornis_inornatus,Rhadina_sibilatrix,Rhagologus_leucostigma,Rhea_americana,Rhea_pennata,Rhegmatorhina_hoffmannsi,Rhinopomastus_cyanomelas,Rhinoptilus_africanus,Rhipidura_dahli,Rhodinocichla_rosea,Rhynochetos_jubatus,Rissa_tridactyla,Rostratula_benghalensis,Rynchops_niger,Sagittarius_serpentarius,Sakesphorus_luctuosus,Sapayoa_aenigma,Saxicola_maurus,Sclerurus_mexicanus,Scopus_umbretta,Scytalopus_superciliaris,Semnornis_frantzii,Serilophus_lunatus,Serinus_canaria,Setophaga_coronata,Setophaga_kirtlandii,Sinosuthora_webbiana,Sitta_europaea,Smithornis_capensis,Spizaetus_tyrannus,Spizella_passerina,Sporophila_hypoxantha,Steatornis_caripensis,Stercorarius_parasiticus,Sterrhoptilus_dennistouni,Strix_occidentalis,Struthidea_cinerea,Struthio_camelus,Sturnus_vulgaris,Sula_dactylatra,Sylvia_atricapilla,Sylvia_borin,Sylvietta_virens,Syrrhaptes_paradoxus,Tachuris_rubrigastra,Taeniopygia_guttata,Tauraco_erythrolophus,Thalassarche_chlororhynchos,Thinocorus_orbignyianus,Thryothorus_ludovicianus,Tichodroma_muraria,Tinamus_guttatus,Todus_mexicanus,Toxostoma_redivivum,Tricholaema_leucomelas,Trogon_melanurus,Turnix_velox,Tympanuchus_cupido,Tyrannus_savana,Tyto_alba,Upupa_epops,Uria_aalge,Uria_lomvia,Urocolius_indicus,Urocynchramus_pylzowi,Vidua_chalybeata,Vidua_macroura,Vireo_altiloquus,Xiphorhynchus_elegans,Zapornia_atra,Zonotrichia_albicollis,Zosterops_hypoxanthus,Zosterops_lateralis, https://cgl.gi.ucsc.edu/data/cactus/363-avian-2020-hub/documentation/b10kHubDescription.html
https://cgl.gi.ucsc.edu/data/cactus/605-vertebrate-2020-hub/hub.txt Mammal and Bird Alignment (605 species) Mammal and Bird Alignment (605 species) 2022-01-18 16:12:17 605 Homo_sapiens,Gallus_gallus,Acanthisitta_chloris,Acrocephalus_arundinaceus,Aegithalos_caudatus,Aegotheles_bennettii,Agapornis_roseicollis,Agelaius_phoeniceus,Alaudala_cheleensis,Alca_torda,Aleadryas_rufinucha,Alectura_lathami,Alopecoenas_beccarii,Amazona_guildingii,Anas_platyrhynchos,Anas_zonorhyncha,Anhinga_anhinga,Anhinga_rufa,Anser_cygnoid,Anseranas_semipalmata,Anthoscopus_minutus,Antrostomus_carolinensis,Apaloderma_vittatum,Aphelocoma_coerulescens,Aptenodytes_forsteri,Apteryx_australis,Apteryx_haastii,Apteryx_owenii,Apteryx_rowi,Aquila_chrysaetos,Aramus_guarauna,Ardeotis_kori,Arenaria_interpres,Asarcornis_scutulata,Atlantisia_rogersi,Atrichornis_clamosus,Balaeniceps_rex,Balearica_regulorum,Baryphthengus_martii,Bombycilla_garrulus,Brachypodius_atriceps,Brachypteracias_leptosomus,Bucco_capensis,Buceros_rhinoceros,Bucorvus_abyssinicus,Buphagus_erythrorhynchus,Burhinus_bistriatus,Cairina_moschata,Calcarius_ornatus,Calidris_pugnax,Callaeas_wilsoni,Callipepla_squamata,Caloenas_nicobarica,Calonectris_borealis,Calypte_anna,Calyptomena_viridis,Campylorhamphus_procurvoides,Cardinalis_cardinalis,Cariama_cristata,Casuarius_casuarius,Cathartes_aura,Catharus_fuscescens,Centropus_bengalensis,Centropus_unirufus,Cephalopterus_ornatus,Cepphus_grylle,Cercotrichas_coryphaeus,Certhia_brachydactyla,Certhia_familiaris,Cettia_cetti,Ceuthmochares_aereus,Ceyx_cyanopectus,Chaetops_frenatus,Chaetorhynchus_papuensis,Chaetura_pelagica,Charadrius_alexandrinus,Charadrius_vociferus,Chauna_torquata,Chionis_minor,Chlamydotis_macqueenii,Chloroceryle_aenea,Chlorodrepanis_virens,Chloropsis_cyanopogon,Chloropsis_hardwickii,Chordeiles_acutipennis,Chroicocephalus_maculipennis,Chunga_burmeisteri,Ciccaba_nigrolineata,Ciconia_maguari,Cinclus_mexicanus,Circaetus_pectoralis,Cisticola_juncidis,Climacteris_rufus,Cnemophilus_loriae,Cochlearius_cochlearius,Colinus_virginianus,Colius_striatus,Columba_livia,Columbina_picui,Copsychus_sechellarum,Corvus_brachyrhynchos,Corvus_cornix,Corvus_moneduloides,Corythaeola_cristata,Corythaixoides_concolor,Coturnix_japonica,Crotophaga_sulcirostris,Crypturellus_cinnamomeus,Crypturellus_soui,Crypturellus_undulatus,Cuculus_canorus,Daphoenositta_chrysoptera,Dasyornis_broadbenti,Dicaeum_eximium,Dicrurus_megarhynchus,Donacobius_atricapilla,Dromaius_novaehollandiae,Dromas_ardeola,Drymodes_brunneopygia,Dryoscopus_gambensis,Dyaphorophyia_castanea,Edolisoma_coerulescens,Egretta_garzetta,Elachura_formosa,Emberiza_fucata,Eolophus_roseicapillus,Erithacus_rubecula,Erpornis_zantholeuca,Erythrocercus_mccallii,Eubucco_bourcierii,Eudromia_elegans,Eulacestoma_nigropectus,Eurypyga_helias,Eurystomus_gularis,Falco_cherrug,Falco_peregrinus,Falcunculus_frontatus,Ficedula_albicollis,Formicarius_rufipectus,Fregata_magnificens,Fregetta_grallaria,Fulmarus_glacialis,Furnarius_figulus,Galbula_dea,Gavia_stellata,Geococcyx_californianus,Geospiza_fortis,Glareola_pratincola,Glaucidium_brasilianum,Grallaria_varia,Grantiella_picta,Grus_americana,Gymnorhina_tibicen,Halcyon_senegalensis,Haliaeetus_albicilla,Haliaeetus_leucocephalus,Heliornis_fulica,Hemignathus_wilsoni,Hemiprocne_comata,Herpetotheres_cachinnans,Himantopus_himantopus,Hippolais_icterina,Hirundo_rustica,Horornis_vulcanius,Hydrobates_tethys,Hylia_prasina,Hypocryptadius_cinnamomeus,Ibidorhyncha_struthersii,Ifrita_kowaldi,Illadopsis_cleaveri,Indicator_maculatus,Irena_cyanogastra,Jacana_jacana,Junco_hyemalis,Lanius_ludovicianus,Larus_smithsonianus,Leiothrix_lutea,Lepidothrix_coronata,Leptocoma_aspasia,Leptosomus_discolor,Leucopsar_rothschildi,Limosa_lapponica,Locustella_ochotensis,Lonchura_striata,Lophotis_ruficrista,Loxia_curvirostra,Loxia_leucoptera,Machaerirhynchus_nigripectus,Malurus_elegans,Manacus_manacus,Melanocharis_versteri,Meleagris_gallopavo,Melopsittacus_undulatus,Melospiza_melodia,Menura_novaehollandiae,Merops_nubicus,Mesembrinibis_cayennensis,Mesitornis_unicolor,Mionectes_macconnelli,Mohoua_ochrocephala,Molothrus_ater,Motacilla_alba,Myiagra_hebetior,Mystacornis_crossleyi,Neodrepanis_coruscans,Neopipo_cinnamomea,Nesospiza_acunhae,Nestor_notabilis,Nicator_chloris,Nipponia_nippon,Nothocercus_julius,Nothocercus_nigrocapillus,Nothoprocta_ornata,Nothoprocta_pentlandii,Nothoprocta_perdicaria,Notiomystis_cincta,Numida_meleagris,Nyctibius_bracteatus,Nyctibius_grandis,Nycticryphes_semicollaris,Nyctiprogne_leucopyga,Oceanites_oceanicus,Odontophorus_gujanensis,Oenanthe_oenanthe,Onychorhynchus_coronatus,Opisthocomus_hoazin,Oreocharis_arfaki,Oreotrochilus_melanogaster,Origma_solitaria,Oriolus_oriolus,Orthonyx_spaldingii,Oxylabes_madagascariensis,Oxyruncus_cristatus,Pachycephala_philippinensis,Pachyramphus_minor,Pandion_haliaetus,Panurus_biarmicus,Paradisaea_raggiana,Pardalotus_punctatus,Parus_major,Passer_domesticus,Passerina_amoena,Patagioenas_fasciata,Pedionomus_torquatus,Pelecanoides_urinatrix,Pelecanus_crispus,Penelope_pileata,Peucedramus_taeniatus,Phaethon_lepturus,Phaetusa_simplex,Phainopepla_nitens,Phalacrocorax_auritus,Phalacrocorax_brasilianus,Phalacrocorax_carbo,Phalacrocorax_harrisi,Phalacrocorax_pelagicus,Phasianus_colchicus,Pheucticus_melanocephalus,Phoenicopterus_ruber,Phylloscopus_trochilus,Piaya_cayana,Picathartes_gymnocephalus,Picoides_pubescens,Piprites_chloris,Pitta_sordida,Ploceus_nigricollis,Pluvianellus_socialis,Podargus_strigoides,Podiceps_cristatus,Podilymbus_podiceps,Poecile_atricapillus,Polioptila_caerulea,Pomatorhinus_ruficollis,Pomatostomus_ruficeps,Probosciger_aterrimus,Promerops_cafer,Prunella_fulvescens,Prunella_himalayana,Pseudopodoces_humilis,Psilopogon_haemacephalus,Psophia_crepitans,Pterocles_burchelli,Pterocles_gutturalis,Pteruthius_melanotis,Ptilonorhynchus_violaceus,Ptilorrhoa_leucosticta,Pycnonotus_jocosus,Pygoscelis_adeliae,Quiscalus_mexicanus,Ramphastos_sulfuratus,Regulus_satrapa,Rhabdornis_inornatus,Rhadina_sibilatrix,Rhagologus_leucostigma,Rhea_americana,Rhea_pennata,Rhegmatorhina_hoffmannsi,Rhinopomastus_cyanomelas,Rhinoptilus_africanus,Rhipidura_dahli,Rhodinocichla_rosea,Rhynochetos_jubatus,Rissa_tridactyla,Rostratula_benghalensis,Rynchops_niger,Sagittarius_serpentarius,Sakesphorus_luctuosus,Sapayoa_aenigma,Saxicola_maurus,Sclerurus_mexicanus,Scopus_umbretta,Scytalopus_superciliaris,Semnornis_frantzii,Serilophus_lunatus,Serinus_canaria,Setophaga_coronata,Setophaga_kirtlandii,Sinosuthora_webbiana,Sitta_europaea,Smithornis_capensis,Spizaetus_tyrannus,Spizella_passerina,Sporophila_hypoxantha,Steatornis_caripensis,Stercorarius_parasiticus,Sterrhoptilus_dennistouni,Strix_occidentalis,Struthidea_cinerea,Struthio_camelus,Sturnus_vulgaris,Sula_dactylatra,Sylvia_atricapilla,Sylvia_borin,Sylvietta_virens,Syrrhaptes_paradoxus,Tachuris_rubrigastra,Taeniopygia_guttata,Tauraco_erythrolophus,Thalassarche_chlororhynchos,Thinocorus_orbignyianus,Thryothorus_ludovicianus,Tichodroma_muraria,Tinamus_guttatus,Todus_mexicanus,Toxostoma_redivivum,Tricholaema_leucomelas,Trogon_melanurus,Turnix_velox,Tympanuchus_cupido,Tyrannus_savana,Tyto_alba,Upupa_epops,Uria_aalge,Uria_lomvia,Urocolius_indicus,Urocynchramus_pylzowi,Vidua_chalybeata,Vidua_macroura,Vireo_altiloquus,Xiphorhynchus_elegans,Zapornia_atra,Zonotrichia_albicollis,Zosterops_hypoxanthus,Zosterops_lateralis,Acinonyx_jubatus,Acomys_cahirinus,Ailuropoda_melanoleuca,Ailurus_fulgens,Allactaga_bullata,Alouatta_palliata,Ammotragus_lervia,Anoura_caudifer,Antilocapra_americana,Aotus_nancymaae,Aplodontia_rufa,Artibeus_jamaicensis,Ateles_geoffroyi,Balaenoptera_acutorostrata,Balaenoptera_bonaerensis,Beatragus_hunteri,Bison_bison,Bos_indicus,Bos_mutus,Bos_taurus,Bubalus_bubalis,Callicebus_donacophilus,Callithrix_jacchus,Camelus_bactrianus,Camelus_dromedarius,Camelus_ferus,Canis_lupus,Canis_lupus_familiaris,Capra_aegagrus,Capra_hircus,Capromys_pilorides,Carlito_syrichta,Carollia_perspicillata,Castor_canadensis,Catagonus_wagneri,Cavia_aperea,Cavia_porcellus,Cavia_tschudii,Cebus_albifrons,Cebus_capucinus,Ceratotherium_simum,Ceratotherium_simum_cottoni,Cercocebus_atys,Cercopithecus_neglectus,Chaetophractus_vellerosus,Cheirogaleus_medius,Chinchilla_lanigera,Chlorocebus_sabaeus,Choloepus_didactylus,Choloepus_hoffmanni,Chrysochloris_asiatica,Colobus_angolensis,Condylura_cristata,Craseonycteris_thonglongyai,Cricetomys_gambianus,Cricetulus_griseus,Crocidura_indochinensis,Cryptoprocta_ferox,Ctenodactylus_gundi,Ctenomys_sociabilis,Cuniculus_paca,Dasyprocta_punctata,Dasypus_novemcinctus,Daubentonia_madagascariensis,Delphinapterus_leucas,Desmodus_rotundus,Dicerorhinus_sumatrensis,Diceros_bicornis,Dinomys_branickii,Dipodomys_ordii,Dipodomys_stephensi,Dolichotis_patagonum,Echinops_telfairi,Eidolon_helvum,Elaphurus_davidianus,Elephantulus_edwardii,Ellobius_lutescens,Ellobius_talpinus,Enhydra_lutris,Eptesicus_fuscus,Equus_asinus,Equus_caballus,Equus_przewalskii,Erinaceus_europaeus,Erythrocebus_patas,Eschrichtius_robustus,Eubalaena_japonica,Eulemur_flavifrons,Eulemur_fulvus,Felis_catus,Felis_nigripes,Fukomys_damarensis,Galeopterus_variegatus,Giraffa_tippelskirchi,Glis_glis,Gorilla_gorilla,Graphiurus_murinus,Helogale_parvula,Hemitragus_hylocrius,Heterocephalus_glaber,Heterohyrax_brucei,Hippopotamus_amphibius,Hipposideros_armiger,Hipposideros_galeritus,Hyaena_hyaena,Hydrochoerus_hydrochaeris,Hystrix_cristata,Ictidomys_tridecemlineatus,Indri_indri,Inia_geoffrensis,Jaculus_jaculus,Kogia_breviceps,Lasiurus_borealis,Lemur_catta,Leptonychotes_weddellii,Lepus_americanus,Lipotes_vexillifer,Loxodonta_africana,Lycaon_pictus,Macaca_fascicularis,Macaca_mulatta,Macaca_nemestrina,Macroglossus_sobrinus,Mandrillus_leucophaeus,Manis_javanica,Manis_pentadactyla,Marmota_marmota,Megaderma_lyra,Mellivora_capensis,Meriones_unguiculatus,Mesocricetus_auratus,Mesoplodon_bidens,Microcebus_murinus,Microgale_talazaci,Micronycteris_hirsuta,Microtus_ochrogaster,Miniopterus_natalensis,Miniopterus_schreibersii,Mirounga_angustirostris,Mirza_coquereli,Monodon_monoceros,Mormoops_blainvillei,Moschus_moschiferus,Mungos_mungo,Murina_feae,Mus_caroli,Mus_musculus,Mus_pahari,Mus_spretus,Muscardinus_avellanarius,Mustela_putorius,Myocastor_coypus,Myotis_brandtii,Myotis_davidii,Myotis_lucifugus,Myotis_myotis,Myrmecophaga_tridactyla,Nannospalax_galili,Nasalis_larvatus,Neomonachus_schauinslandi,Neophocaena_asiaeorientalis,Noctilio_leporinus,Nomascus_leucogenys,Nycticebus_coucang,Ochotona_princeps,Octodon_degus,Odobenus_rosmarus,Odocoileus_virginianus,Okapia_johnstoni,Ondatra_zibethicus,Onychomys_torridus,Orcinus_orca,Orycteropus_afer,Oryctolagus_cuniculus,Otolemur_garnettii,Ovis_aries,Ovis_canadensis,Pan_paniscus,Pan_troglodytes,Panthera_onca,Panthera_pardus,Panthera_tigris,Pantholops_hodgsonii,Papio_anubis,Paradoxurus_hermaphroditus,Perognathus_longimembris,Peromyscus_maniculatus,Petromus_typicus,Phocoena_phocoena,Piliocolobus_tephrosceles,Pipistrellus_pipistrellus,Pithecia_pithecia,Platanista_gangetica,Pongo_abelii,Procavia_capensis,Propithecus_coquereli,Psammomys_obesus,Pteronotus_parnellii,Pteronura_brasiliensis,Pteropus_alecto,Pteropus_vampyrus,Puma_concolor,Pygathrix_nemaeus,Rangifer_tarandus,Rattus_norvegicus,Rhinolophus_sinicus,Rhinopithecus_bieti,Rhinopithecus_roxellana,Rousettus_aegyptiacus,Saguinus_imperator,Saiga_tatarica,Saimiri_boliviensis,Scalopus_aquaticus,Semnopithecus_entellus,Sigmodon_hispidus,Solenodon_paradoxus,Sorex_araneus,Spermophilus_dauricus,Spilogale_gracilis,Suricata_suricatta,Sus_scrofa,Tadarida_brasiliensis,Tamandua_tetradactyla,Tapirus_indicus,Tapirus_terrestris,Thryonomys_swinderianus,Tolypeutes_matacus,Tonatia_saurophila,Tragulus_javanicus,Trichechus_manatus,Tupaia_chinensis,Tupaia_tana,Tursiops_truncatus,Uropsilus_gracilis,Ursus_maritimus,Vicugna_pacos,Vulpes_lagopus,Xerus_inauris,Zalophus_californianus,Zapus_hudsonius,Ziphius_cavirostris, https://cgl.gi.ucsc.edu/data/cactus/605-vertebrate-2020-hub/documentation/600wayHubDescription.html
https://cotneylab.cam.uchc.edu/~jcotney/CRANIOFACIAL_HUB/Craniofacial_Data_Hub.txt Cotney Lab Human Craniofacial Epigenomics Human Embryonic Craniofacial Tissue Epigenomic Data and Chromatin State Segmentations from the Cotney Lab at UConn Health 2017-04-27 09:23:33 3 hg19,mm9,hg38, http://cotney.research.uchc.edu
https://danio-code.zfin.org/trackhub/DANIO-CODE.hub.txt DANIO-CODE Track Hub DANIO-CODE: Central repository for zebrafish genomic datasets 2020-06-03 10:51:46 2 danRer10,danRer11, https://danio-code.zfin.org/trackhubDescription/
https://dashr2.lisanwanglab.org/tracks/DASHR2_hub.txt DASHR v2.0 Hub DASHR v2.0 Human small non-coding RNA data hub 2018-12-05 11:09:59 2 hg19,hg38, http://lisanwanglab.org/DASHRv2/
https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/hub.txt PhyloCSF Evolutionary protein-coding potential as measured by PhyloCSF 2015-01-06 13:50:19 9 hg19,hg38,mm10,mm39,galGal4,galGal6,dm6,ce11,wuhCor1, https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/hub.DOC.html
https://data.broadinstitute.org/compbio1/SynonymousConstraintTracks/trackHub/hub.txt Synonymous Constraint Synonymous Constraint Elements and Synonymous Acceleration Elements in protein-coding regions 2020-02-07 11:48:59 3 hg19,hg38,wuhCor1, https://data.broadinstitute.org/compbio1/SynonymousConstraintTracks/trackHub/SynonymousConstraint.html
https://data.broadinstitute.org/vgb/dog/dog/hub.txt Broad Improved Canine Annotation v1 Broad Institute CanFam3 Improved Annotation Data v1 2017-05-16 10:54:10 1 canFam3, http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0091172
https://data.cyverse.org/dav-anon/iplant/home/juanlmateo/CISSTEM/hub.txt Seq-data on mm9 NS5 cells Set of sequencing data on mm9 NS5 cells 2017-11-28 08:32:43 1 mm9, http://genome.cshlp.org/content/25/1/41.full
https://data.cyverse.org/dav-anon/iplant/home/samksmith/steguina_track-hub/steguina/hub.txt singing mouse genome hub This is the genome hub for Alston's singing mouse (Scotinomys teguina) 2022-02-14 10:41:41 1 steguina, https://data.cyverse.org/dav-anon/iplant/home/samksmith/steguina_track-hub/steguina/aboutHub.html
https://downloads.wormbase.org/releases/current-production-release/MULTI_SPECIES/hub/hub.txt WormBase WormBase nematode genomes 2017-02-10 11:57:55 12 brenneri,japonica,remanei,ovolvulus,briggsae,brugia,brugia3,c_nigoni,pristionchus,t_muris,elegans,s_ratti, https://downloads.wormbase.org/releases/current-production-release/MULTI_SPECIES/hub/documentation/hub.html
https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt EPD Viewer Hub Promoter specific experimental data and TSS annotation from the EPD database 2017-01-23 13:00:37 18 hg19,hg38,mm9,mm10,danRer7,rheMac8,galGal5,rn6,canFam3,dm6,amel5,ce6,sacCer3,spo2,pfa2,araTha1,zm3,dpu2, https://epd.expasy.org/epd/
https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/hub.txt dbVar Hub NCBI's database of human genomic Structural Variation -- large variants >50 bp 2020-03-30 09:06:34 2 hg19,hg38, https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/dbVar.html
https://ftp.ncbi.nlm.nih.gov/refseq/FunctionalElements/trackhub/hub.txt RefSeqFE Hub NCBI RefSeq Functional Elements interactions and features 2020-08-07 17:14:22 6 GCA_009914755.4,hg19,hg38,hs1,mm10,mm39, https://ftp.ncbi.nlm.nih.gov/refseq/FunctionalElements/trackhub/RefSeqFE_Hub.html
https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/hub.txt ALFA Hub NCBI's Allele Frequency Aggregator (ALFA) allele frequency for variants in dbGaP studies. 2020-09-02 16:46:09 2 hg19,hg38, https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/latest/ALFA.html
https://genome-test.gi.ucsc.edu/hubs/globalReference/hub.txt Human Global Reference Genomes Human Global Reference Genome assembly hub 2020-01-20 15:42:49 10 GCA_003601015.1_HG03807_prelim_1.0,GCA_003574075.1_HG02818_prelim_1.0,GCA_003086635.1_HG03486_prelim_1.0,GCA_003070785.1_HG02059_prelim_1.0,GCA_002872155.1_NA19434_prelim_1.0,GCA_002209525.2_HG01352_prelim_2.1,GCA_002208065.1_HG00733_prelim_1.0,GCA_002180035.3_HG00514_prelim_3.0,GCA_002077035.3_NA12878_prelim_3.0,GCA_001524155.4_NA19240_prelim_3.0, https://genome-test.gi.ucsc.edu/hubs/globalReference/index.html
https://genome-test.gi.ucsc.edu/~max/immuno/track/hub/hub.txt Cancer Genomics Tracks TCGA and ICGC Cancer Mutations, TCGA Expression, Immune Epitopes Database (IEDB), Cancer Immunity Peptides Database, Dienstmann Variant/Cancer database, CIVIC, MyCancerGenome.org, OncoKB 2016-01-10 18:42:09 1 hg19, https://genome-test.gi.ucsc.edu/~max/immuno/track/hub/desc.html
https://hgdownload.soe.ucsc.edu/hubs/CCGP/hub.txt CCGP The California Conservation Genomics Project (CCGP) assemblies 2023-05-03 14:40:12 126 GCA_026170555.1,GCA_026170545.1,GCA_024610745.1,GCA_024610735.1,GCA_022747625.1,GCA_022747635.1,GCA_025532165.1,GCA_026230005.1,GCA_026230025.1,GCA_028538565.1,GCA_028534965.1,GCA_019985065.2,GCA_019985075.1,GCA_022045225.1,GCA_022045235.1,GCA_028534865.1,GCA_028534895.1,GCA_022578405.1,GCA_022577435.1,GCA_026167975.1,GCA_026167985.1,GCA_022079275.1,GCF_022079265.1,GCA_024803775.1,GCA_024803745.1,GCA_022605925.1,GCA_022605575.1,GCA_023349545.1,GCA_023349395.1,GCA_022578425.1,GCA_022577455.1,GCF_021869535.1,GCA_021869935.1,GCA_023055725.1,GCA_023055505.1,GCA_028535905.1,GCA_028535815.1,GCA_022749735.1,GCA_022749685.1,GCA_028537955.1,GCA_028537755.1,GCA_029215685.1,GCA_029215655.1,GCA_023055485.1,GCA_023055345.1,GCA_028535165.1,GCA_028535515.1,GCA_024363435.1,GCA_024363575.1,GCA_024610695.1,GCA_024610705.1,GCA_024711535.1,GCA_024711525.1,GCA_023349535.1,GCA_023349555.1,GCA_026229955.1,GCA_026167925.1,GCA_029215635.1,GCA_029215605.1,GCA_023362785.1,GCA_023362775.1,GCA_022086895.1,GCA_022086475.1,GCA_028749965.1,GCA_028749985.1,GCA_023055495.1,GCF_023055435.1,GCA_023053685.1,GCA_021966175.1,GCA_021963965.1,GCA_029215795.1,GCA_029215775.1,GCA_023333555.1,GCA_023333525.1,GCA_023053675.1,GCA_023053635.1,GCA_023053665.1,GCA_023055565.1,GCA_023055425.1,GCA_022578375.1,GCA_022577445.1,GCA_022749775.1,GCA_022749695.1,GCA_024509165.1,GCA_024509115.1,GCA_023634275.1,GCA_023634205.1,GCA_023349385.1,GCA_023349425.1,GCA_023634265.1,GCA_023634235.1,GCA_026168045.1,GCA_026167965.1,GCA_026437355.1,GCA_026437365.1,GCA_026230055.1,GCA_026230045.1,GCA_024363235.1,GCA_024362995.1,GCA_023055385.1,GCA_023055355.1,GCA_029207655.1,GCA_029207665.1,GCA_023053535.1,GCA_023053565.1,GCA_023053555.1,GCA_023053575.1,GCA_023053545.1,GCA_022605895.1,GCA_022605955.1,GCA_023333635.1,GCA_023333645.1,GCA_026170595.1,GCA_026170395.1,GCA_028536645.1,GCA_028536675.1,GCA_029215705.1,GCA_029215755.1,GCA_023055415.1,GCA_023055335.1,GCA_029207785.1,GCA_029207755.1,GCA_024372515.1,GCA_024362935.1,GCA_028536395.1,GCA_028538775.1, https://hgdownload.soe.ucsc.edu/hubs/CCGP/index.html
https://hgdownload.soe.ucsc.edu/hubs/HPRC/hub.txt HPRC The Human Pangenome Reference Consortium 2023-05-03 15:15:53 96 GCA_018471515.1,GCA_018472595.1,GCA_018472605.1,GCA_018472575.1,GCA_018472565.1,GCA_018472585.1,GCA_018506975.1,GCA_018506955.1,GCA_018472765.1,GCA_018472715.1,GCA_018471095.1,GCA_018471105.1,GCA_018472685.1,GCA_018472725.1,GCA_018471345.1,GCA_018471075.1,GCA_018504365.1,GCA_018504645.1,GCA_018469665.1,GCA_018469695.1,GCA_018471085.1,GCA_018471065.1,GCA_018504375.1,GCA_018504045.1,GCA_018469405.1,GCA_018469675.1,GCA_018469865.1,GCA_018469965.1,GCA_018469685.1,GCA_018469705.1,GCA_018467155.1,GCA_018467165.1,GCA_018472695.1,GCA_018472705.1,GCA_018471545.1,GCA_018471555.1,GCA_018472865.1,GCA_018472845.1,GCA_018506125.1,GCA_018505855.1,GCA_018504085.1,GCA_018504055.1,GCA_018505825.1,GCA_018505865.1,GCA_018852585.1,GCA_018852595.1,GCA_018471535.1,GCA_018471525.1,GCA_018466845.1,GCA_018466835.1,GCA_018467015.1,GCA_018467005.1,GCA_018466985.1,GCA_018466855.1,GCA_018470445.1,GCA_018470435.1,GCA_018469875.1,GCA_018469925.1,GCA_018469955.1,GCA_018469945.1,GCA_018469935.1,GCA_018470425.1,GCA_018504065.1,GCA_018504075.1,GCA_018503585.1,GCA_018503575.1,GCA_018470455.1,GCA_018470465.1,GCA_018506165.1,GCA_018506155.1,GCA_018472855.1,GCA_018473305.1,GCA_018503525.1,GCA_018503245.1,GCA_018505845.1,GCA_018505835.1,GCA_018469425.1,GCA_018469415.1,GCA_018473295.1,GCA_018473315.1,GCA_018472825.1,GCA_018472835.1,GCA_018503255.1,GCA_018503285.1,GCA_018503275.1,GCA_018503265.1,GCA_018504635.1,GCA_018504625.1,GCA_018504655.1,GCA_018504665.1,GCA_021951015.1,GCA_021950905.1,GCA_018852615.1,GCA_018852605.1,GCA_018506965.1,GCA_018506945.1, https://hgdownload.soe.ucsc.edu/hubs/HPRC/index.html
https://hgdownload.soe.ucsc.edu/hubs/RepeatBrowser2020/hub.txt UCSC Repeat Browser 2020 Update Human Repeat consensuses annotated with lifted tracks 2020-03-18 11:59:31 3 hg38reps,hg19,hg38, http://repeatbrowser.ucsc.edu
https://hgdownload.soe.ucsc.edu/hubs/enigma/hub.txt ENIGMA BRCA1/BRCA2 specs 1.1.0 ENIGMA BRCA1/BRCA2 Panel Specifications of ACMG/AMP Guidelines version 1.1.0 2024-08-28 15:24:37 2 hg38,hg19, https://hgdownload.soe.ucsc.edu/hubs/enigma/enigma.html
https://hgdownload.soe.ucsc.edu/hubs/methbase/v1/hub.txt MethBase (Legacy) MethBase: 605 DNA Methylation profiles reprocessed from NCBI SRA 2013-05-28 15:13:19 14 hg38,canFam3,panTro2,hg18,rheMac8,danRer11,danRer7,panTro4,mm10,mm9,hg19,ponAbe2,rn5,rheMac3, https://hgdownload.soe.ucsc.edu/hubs/methbase/v1/description.html
https://hpc.nih.gov/eyebrowse/hub.txt EyeBrowse Eye tissue specific genes and markers, derived from NEIBank and other sources 2022-01-21 14:30:15 12 hg19,bosTau6,canFam2,cavPor3,danRer6,danRer7,rn4,rheMac2,galGal3,hg17,hg18,mm9, https://hpc.nih.gov/eyebrowse/description.html
https://krishna.gs.washington.edu/download/CADD/bigWig/CADD-browserTracks/hub.txt CADD CADD Track for v1.3 to v1.7 2020-03-19 13:45:37 2 hg19,hg38, https://krishna.gs.washington.edu/download/CADD/bigWig/CADD-browserTracks/readme.md
https://mutscore-ucsc.iob.ch/hub.txt MutScore Variant Pathogenicity MutScore Variant Pathogenicity 2023-08-16 14:05:03 2 hg38,hg19, https://doi.org/10.1016/j.ajhg.2022.01.006
https://orio.niehs.nih.gov/ucscview/nguyen/p53BAER/hub.txt human p53 Binding And Expression Resource (BAER) hub human p53 ChIP-seq coverage depth (tracks) & SISSRs peak calls with associated differential gene expression from published data as of May 2015 2018-10-26 14:32:27 1 hg19, https://orio.niehs.nih.gov/ucscview/nguyen/p53BAER/p53BAER.html
https://pikedata.biochem.wisc.edu/GSE79815_MSC_HUB/hub.txt ChIP-seq data track HUBs from MSC cells from GSE79815 ChIP-seq data from the publication "Epigenetic plasticity drives adipogenic and osteogenic differentiation of marrow-derived mesenchymal stem cells" (10.1074/jbc.M116.736538) from GEO record GSE79815 2016-08-23 16:07:37 1 mm9, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79815
https://pmgenomics.ca/hoffmanlab/proj/bismap/trackhub/hub.txt Umap and Bismap mappability Uniquely mappable regions of genome and methylome 2016-12-22 07:30:07 4 hg38,hg19,mm9,mm10, https://bismap.hoffmanlab.org/trackhub/index.html
https://raw.githubusercontent.com/AndyMSSMLab/UCSC_exp_meth_VNTR/main/hub.txt Exp/Meth VNTR hub Association of VNTRs with Expression and Methylation in GTEx, PCGC and PPMI 2021-01-21 12:17:21 2 hg19,hg38, https://gargp01.u.hpc.mssm.edu/ucsc_exp_meth_vntr.html
https://raw.githubusercontent.com/BieseckerLab/PolyAProject/master/files/myHub/hub.txt Predominant PAS and predominant hexamers Predominant polyA sites and predominant hexamers 2023-08-29 16:23:28 2 hg38,hg19, https://pubmed.ncbi.nlm.nih.gov/37606238/
https://raw.githubusercontent.com/Iuliana-Ionita-Laza/Colocalization_tracks/master/hub.txt Coloc segments Colocalized segments of human genome for Roadmap cell types 2020-02-27 13:01:32 1 hg19, http://www.funlda.com/colocalization/track
https://raw.githubusercontent.com/Kraus-Lab/publichubs/master/breast_cancer_lncrna_pmid_26236012/hub.txt Breast Cancer lncRNA Breast Cancer lncRNA PMID 26236012 2019-02-19 09:43:06 1 hg19, https://www.ncbi.nlm.nih.gov/pubmed/26236012.html
https://raw.githubusercontent.com/ScrippsPipkinLab/GenomeTracks/main/hub.txt T_cell_ATAC_ChIP_Pipkin T cell ATACseq ChIPseq assembly by Pipkin lab 2020-12-10 10:48:52 1 mm10, https://github.com/ScrippsPipkinLab/GenomeTracks
https://raw.githubusercontent.com/aharon-weizmann/Corona-ORFs/master/final/hub.txt ORF Predictions RNA-Seq, Ribo_Seq, and ORF Predictions 2020-09-15 18:29:57 1 wuhCor1, https://raw.githubusercontent.com/aharon-weizmann/Corona-ORFs/master/final/docs/ORFs_predic.html
https://raw.githubusercontent.com/alona-korzhakova/ucsc_genome_browser/master/data/conf/hub.txt IMPACT regulatory element activity Cell-type-specific regulatory element activity profiles across 707 unique combinations of transcription factor-cell type pairs. IMPACT predicts the epigenetic regulatory activity related to a particular transcription factor in a given cell type. IMPACT sc 2024-02-23 11:45:17 1 hg19, https://www.amariutalab.org/genomebrowser
https://raw.githubusercontent.com/csaueres/fairbrothertrack/master/hub.txt Splice Site Usage Hub Splice Site Usage Values Calculated for 19 ENCODE Cell Lines from RNA-seq 2020-02-25 11:37:45 1 hg19, https://vivo.brown.edu/display/wfairbro#Research
https://raw.githubusercontent.com/drozdovapb/PeterhofYeastHub/master/hub.txt Peterhof_yeasts Peterhof_yeast 2016-01-25 08:38:35 12 sacCer3,1B_D1606_spades,1B_D1606_chromosomer,15V_P4_spades,15V_P4_chromosomer,25_25_2V_P3982_spades,25_25_2V_P3982_chromosomer,74_D964_spades,74_chromosomer,15V_P4_test,6P_33G_D373_spades,6P_33G_D373_chromosomer, https://raw.githubusercontent.com/drozdovapb/PeterhofYeastHub/master/hub_contents.html
https://raw.githubusercontent.com/mhalushka/UCSC_miRNA_barchart/master/hub.txt Human cellular microRNAome barCharts Evaluation of >10 billion small RNA-seq reads from 78 primary cell types and 42 cancer or immortalized cell lines from 3 main studies. 2017-09-11 08:08:46 1 hg38, http://genome.cshlp.org/content/early/2017/09/06/gr.222067.117.long
https://raw.githubusercontent.com/mhalushka/miROme/main/UCSC/hub.txt ABC of cellular microRNAome Advanced BarChart configuration of cellular microRNAome. Evaluation of >20 billion small RNA-seq reads from 196 primary cell types (+plasma, +platelets) across 175 main studies. 2022-03-11 15:17:57 1 hg38, https://raw.githubusercontent.com/arunhpatil/miROme/main/UCSC/description.html
https://remap.univ-amu.fr/storage/public/hubReMap2022/hub.txt ReMap 2022 Regulatory Atlas ReMap 2022: A database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments Go to ReMap2022 for more info. 2021-09-02 13:12:54 6 mm10,mm39,hg38,hg19,dm6,araTha1, https://remap.univ-amu.fr/storage/public/hubReMap2022/remapHub2022.html
https://resources.altius.org/~jvierstra/projects/footprinting.2020/hub.txt Digital genomic footprinting (Vierstra et al., 2020) Digital genomic footprinting from 243 cell & tissue types 2020-08-28 10:05:54 1 hg38, https://resources.altius.org/~jvierstra/projects/footprinting.2020/trackhub/description.html
https://s3-us-west-2.amazonaws.com/croc-paper-hub/hub.txt Croc and Bird Hub Croc, Bird, and Archosaur Assembly Hub 2014-10-20 08:45:50 45 allMis2,Anc00,Anc01,Anc02,Anc03,Anc04,Anc06,Anc07,Anc08,Anc09,Anc10,Anc11,Anc12,Anc13,Anc14,Anc15,Anc16,Anc17,Anc18,Anc19,Anc20,Anc21,Anc05,melUnd1,galGal4,ficAlb2,croPor2,ghaGan1,cheMyd1,anoCar2,anaPla1,geoFor1,strCam0,chrPic1,amaVit1,falPer1,colLiv1,falChe1,araMac1,pelSin1,apaSpi1,pseHum1,melGal1,zonAlb1,taeGut2, NULL
https://s3.amazonaws.com/DLPFC_n36/humanDLPFC/hub.txt LIBD Human DLPFC Development RNAseq data across human brain development by age group from LIBD 2015-03-02 11:38:06 1 hg19, http://www.libd.org
https://s3.mpi-bn.mpg.de/data-tobias-ucsc/hub.txt TOBIAS footprint prediction Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal 2020-05-06 15:30:35 2 hg38,mm10, https://s3.mpi-bn.mpg.de/data-tobias-ucsc/README.html
https://s3.us-east-2.amazonaws.com/brainepigenome/hub.txt BrainEpigenomeHub DNA methylation, chromatin accessibility, and gene expression data from NeuN flow-sorted human brain samples 2018-05-30 10:41:01 1 hg19, https://s3.us-east-2.amazonaws.com/brainepigenome/hg19/docs/README.html
https://storage.googleapis.com/gcp.wenglab.org/hubs/dna20/hub.txt ENCODE DNA Trackhub ENCODE Trackhub for DNA-based assays 2020-10-05 16:03:03 3 hg19,hg38,mm10, https://storage.googleapis.com/gcp.wenglab.org/hubs/dna20/description.html
https://storage.googleapis.com/gcp.wenglab.org/hubs/integrative52/hub.txt ENCODE integrative Trackhub ENCODE Trackhub for integrative results 2020-10-05 16:01:44 2 hg38,mm10, https://storage.googleapis.com/gcp.wenglab.org/hubs/integrative52/hub.html
https://storage.googleapis.com/gcp.wenglab.org/hubs/rna22/hub.txt ENCODE RNA Trackhub ENCODE Trackhub for RNA-based assays 2020-10-05 16:00:34 3 hg19,hg38,mm10, https://storage.googleapis.com/gcp.wenglab.org/hubs/rna22/hub.html
https://trackhubs.uniprot.org/genome_annotation_tracks/UP000005640_9606_hub/hub.txt UniProt Features UniProtKB reviewed protein features mapped to the Ensembl genome assembly. 2016-08-16 12:05:14 1 hg38, http://nar.oxfordjournals.org/content/43/D1/D204
https://unibind.uio.no/static/data/latest/UniBind_hubs_Permissive/UCSC/hub.txt UniBind 2021 permissive Hub UniBind 2021 hub for permissive direct TF-DNA interactions 2021-01-14 10:22:40 9 hg38,mm10,ce11,dm6,danRer11,spo2,sacCer3,rn6,araTha1, https://unibind.uio.no/static/data/latest/UniBind_hubs_Permissive/UCSC/UniBind.html
https://unibind.uio.no/static/data/latest/UniBind_hubs_Robust/UCSC/hub.txt UniBind 2021 Robust Hub UniBind 2021 hub for robust direct TF-DNA interactions 2021-01-14 10:21:35 8 hg38,mm10,ce11,dm6,danRer11,sacCer3,rn6,araTha1, https://unibind.uio.no/static/data/latest/UniBind_hubs_Robust/UCSC/UniBind.html
https://unibind2018.uio.no/static/data/20190717/UniBind_hubs_Permissive/UCSC/hub.txt UniBind 2018 Hub UniBind: A map of direct TF-DNA interactions from ChIP-seq and TF binding profiles 2019-04-12 09:15:57 1 hg38, https://unibind2018.uio.no/static/data/20190717/UniBind_hubs_Permissive/UCSC/UniBind.html
https://vizhub.wustl.edu/VizHub/RoadmapIntegrative.txt Roadmap Epigenomics Integrative Analysis Hub Roadmap Epigenomics Integrative Analysis Hub at Washington University in St. Louis 2014-05-16 15:42:42 1 hg19, http://www.roadmapepigenomics.org/
https://vizhub.wustl.edu/VizHub/RoadmapReleaseAll.txt Roadmap Epigenomics Data Complete Collection at Wash U VizHub Roadmap Epigenomics Human Epigenome Atlas Data Complete Collection, VizHub at Washington University in St. Louis 2012-02-10 16:34:08 2 hg19,hg38, http://www.roadmapepigenomics.org/
https://www.dfam.org/web_download/DfamHub/hub.txt Dfam database of TE families and annotations Dfam database of Transposable Element families and genome annotations 2022-02-08 11:55:01 1 hg38, https://www.dfam.org/web_download/DfamHub/DfamHub.html
https://www.facebase.org/trackhub/hub.txt FaceBase Hub Comprehensive craniofacial research data from FaceBase.org 2016-12-16 13:49:31 4 mm9,mm10,hg18,hg19, https://www.facebase.org
https://www.lncipedia.org/trackhub/hub.txt LNCipedia 5.2 LNCipedia 5.2 - A comprehensive compendium of human long non-coding RNAs 2018-03-22 15:38:35 2 hg19,hg38, https://www.lncipedia.org/trackhub/docs/description.html