ORTHOSCOPE v1.5.8: Plants
Gene tree and orthogroup estimation using a species tree (< 5 min as default). 28 Nov. 2025
Instructions, Species tree Support: Safari, Firefox, Chrome yurai
Focal group    
Actinopterygians Mammals Vertebrates Deuterostomes Protostomes Acropora Plants
Status
Ready.
 
Mode Estimate gene tree Compare gene and species trees Download gene models
Query sequences (fasta format): DNA  Amino acid  Example fasta file:
RH20 DNA: Arabidopsis, Oryza; Amino acid: Arabidopsis
 
  Species tree (newick): If not selected, this tree is used.
Sequence collection
E-value threshold for reported sequences 1e-5   1e-4   1e-3   1e-2   1e-1   1
Number of BLAST hits to report per genome 3   5   10   20
Alignment
Aligned site rate threshold
 within unambiguously aligned sites		 0   0.2   0.4   0.55
Tree search
Dataset Amino acid
  DNA (Exclude 3rd)   DNA (Include 3rd)
Rearrangement BS value threshold 60%   70%   80%
Key node Magnoliopsida or Mesangiospermae
Node name in rearranged gene tree BSvalue   BSvalue_Classification_DupState  
Gene description in gene tree leaf Shown   Not shown  
Genome taxon sampling
Example: Oryza, Jiao11FigS2.
If the file is not uploaded, the following taxon sampling is used.  
 Classification  Scientific name  Common name  Data source  DB  Genes
Bacteria
      Streptomycetaceae Kitasatospora-setae KM-6054 EnsBac62 p, n 7578
  Streptomyces-griseus NBRC 13350 EnsBac62 p, n 7097
  Streptomyces-coelicolor S.coelicolor A3(2) EnsBac42 p, n 8154
Opisthokonta
   Fungi Sclerotinia-sclerotiorum Ascomycetes EnsFun42 p, n 10175
  Saccharomyces-cerevisiae Baker's yeast Ens92 p, n 6692
  Saccharomyces-cerevisiae-1 Baker's yeast RefSeq90 p, n 5983
   Ichthyosporea Sphaeroforma-arctica — RefSeq90 p, n 18213
  Capsaspora-owczarzaki — RefSeq90 p, n 8621
   Choanoflagellida Salpingoeca-rosetta Choanoflagellate RefSeq90 p, n 11624
  Monosiga-brevicollis Choanoflagellate RefSeq90 p, n 9171
   Metazoa Drosophila-melanogaster Fruit fly EnsMet38 p, n 13931
  Oikopleura-dioica Pelagic tunicate OikoBase p, n 17212
  Ciona-savignyi Pacific transparent sea squirt Ens91 p, n 11616
  Ciona-intestinalis-KY21 Transparent sea squirt Ghost KY21 p, n 18788
  Homo-sapiens-E102 Human Ens102 p, n 23483
Sar
   Alveolata
      Symbiodiniaceae
         Clade D Durusdinium-trenchii Dinoflagellate OIST p, n 33775
         Clade A Symbiodinium-minutum Dinoflagellate OIST
  Symbiodinium-microadriaticum Dinoflagellate EnsProt44 p, n 43403
   Phaeophyceae (brown algae)
      Ectocarpales
         Ectocarpaceae Ectocarpus-siliculosus Maiden's hair NCBI p, n 16267
         Chordariaceae Nemacystus-decipiens Ito mozuku OIST p, n 17736
  Cladosiphon-okamuranus-K Okinawa mozuku St.K OIST p, n 27936
  Cladosiphon-okamuranus-O Okinawa mozuku St.O OIST p, n 46677
  Cladosiphon-okamuranus-C Okinawa mozuku St.C OIST p, n 22487
  Cladosiphon-okamuranus-S Okinawa mozuku St.S v2 OIST p, n 21113
Rhodophyta (red algae)
   Florideophyceae Chondrus-crispus Irish moss EnsPla62 p, n 9807
   Bangiophyceae
      Galdieriales Galdieria-sulphuraria Extremophilic red alga EnsPla62 p, n 6622
      Cyanidiales Cyanidioschyzon-merolae Red algae EnsPla62 p, n 4973
             
Haptophyta            
   Pavlovophyceae            
   Prymnesiophyceae Emiliania-huxleyi Coccolithophore EnsProt44 p, n 38544
 
Viridiplantae (green plants)
Chlorophyta (green algae)
   Mamiellophyceae Ostreococcus-lucimarinus Green algae EnsPla58
   Chlorophyceae Chlamydomonas-reinhardtii Chlamydomonas EnsPla62 p, n 17743
   Ulvophyceae Caulerpa-lentillifera Siphonous green alga OIST-S p, n 9311
Streptophyta          
   Charophyceae Chara-braunii Braun's stonewort EnsPla51 p, n 34718
   Zygnematophyceae Penium-margaritaceum Charophyte alga CornellUniv p, n 53262
   Embryophyta (land plants)
      Bryophyta
         Marchantiophyta (liverworts) Marchantia-polymorpha-MpTak1v51 Male Tak1 MarpolBase p, n 23339
  Marchantia-polymorpha-MpTakv61 Male and female MarpolBase p, n 23399
  Marchantia-polymorpha Common liverwort EnsPla51 p, n 19287
         Anthocerotophyta (hornworts) Anthoceros-angustus Hornwort Zhang19 p, n 14629
         Bryopsida (mosses)
            Sphagnophytina Sphagnum-fallax Flat-topped bogmoss Phytozome13 NA <230531
            Bryophytina Ceratodon-purpureus-GG1 Dioicous moss Phytozome13 p, n 39339
  Physcomitrella-patens-V33 Spreading earthmoss Phytozome13 NA <230531
  Physcomitrella-patens Spreading earthmoss EnsPla50 p, n 32234
      Tracheophyta (vascular plants)
            Lycopodiopsida Selaginella-moellendorffii Club mosses EnsPla50 p, n 34799
            Euphyllophyta (megaphyllous plants)
              Polypodiopsida (ferns)
                 Equisetidae
                 Polypodiidae
                   Salviniales
                      Marsileaceae Marsilea-vestita Hairy water-clover FernBase p, n 22541
                      Salviniaceae Azolla-filiculoides Mosquito fern FernBase p, n 20203
  Salvinia-cucullata Asian watermoss FernBase p, n 19779
                   Cyatheales Alsophila-spinulosa Flying spider-monkey tree fern FernBase v3.1 includes bugs
                   Polypodiales
                      Parkerioideae Ceratopteris-richardii Triangle Waterfern FernBase p, n 75253
                      Vittarioideae Adiantum-capillus-veneris Southern maidenhair fern FernBase xxxx
              Spermatophyta (seed plants)
                 Acrogymnospermae (gymnosperms)
                   Ginkgoopsida Ginkgo-biloba Maidenhair tree PLAZA1.0 p, n 30404
                   Cycadopsida Cycas-micholitzii Micholitz sago PLAZA1.0 p, n 28901
                   Coniferae
                      Gnetopsida Gnetum-montanum Gam nui PLAZA1.0 p, n 32549
                      Pinopsida
                        Conifers II
                              Taxaceae Taxus-baccata English yew — p, n 32062
                              Cupressaceae Cryptomeria-japonica Japanese cedar RefSeq040128 p, n 41145
                        Conifers I
                              Pinaceae Pseudotsuga-menziesii Douglas fir PLAZA1.0 p, n 149717
  Picea-glauca White spruce PLAZA1.0 p, n 28909
  Pinus-sylvestris Scots pine PLAZA1.0 p, n 36106
                 Magnoliopsida (angiosperms[flowering plants])
                   Nymphaeales Nymphaea-colorata Water lily EnsPla51 p, n 35831
                   Amborellales Amborella-trichopoda Amborella EnsPla51 p, n 27313
                   Mesangiospermae          
                      Liliopsida (monocotyledon)
                        Dioscoreales Dioscorea-rotundata White Guinea yam EnsPla51 p, n 34551
                        Asparagales Asparagus-officinalis Garden asparagus EnsPla51 p, n 24141
                        commelinids            
                           Zingiberales            
                              Musaceae Musa-acuminata Banana EnsPla51 p, n 35012
                              Zingiberaceae Zingiber-officinale Ginger RefSeq210813 p, n 68068
                           Poales            
                              Bromeliaceae Ananas-comosus Pineapple RefSeq210813 p, n 22166
                              Poaceae          
                                PACMAD clade
                                   Chloridoideae Eragrostis-tef Weeping love grass EnsPla58
                                   Arundinoideae Phragmites-australis Common reed RefSeq240229 p, n 38444
                                   Panicoideae
                                     Panicodae Setaria-italica Foxtail millet EnsPla51 p, n 35831
                                     Andropogoneae
                                        Tripsacinae Zea-mays Corn EnsPla58
                                        Sorghinae Sorghum-bicolor Sorghum EnsPla50 p, n 34118
                                        Saccharinae Saccharum-spontaneum Wild sugarcane EnsPla58
  Saccharum-officinarum Sugar cane  
                                BOP clade
                                   Bambusoideae
                                   Pooideae
                                     Poodae Lolium-perenne Ray grass EnsPla58
                                     Stipodae Brachypodium-distachyon Stiff brome EnsPla53 p, n 34310
                                     Triticodae
                                        Hordeinae Secale-cereale Rye EnsPla53 p, n 34441
  Hordeum-vulgare Barley EnsPla53 p, n 35825
                                        Triticinae Aegilops-tauschii Tausch's goatgrass EnsPla53 p, n 39614
  Triticum-spelta Spelt EnsPla53 p, n 113301
  Triticum-aestivum Bread wheat EnsPla50 p, n 107545
                                   Oryzoideae Leersia-perrieri Cutgrasses EnsPla54 p, n 29078
    Oryza-brachyantha Wild rice EnsPla58
    Oryza-glaberrima African rice EnsPla58
  Oryza-sativa-Japonica Japanese rice EnsPla50 p, n 35775 12
                      Ranunculales Papaver-somniferum Opium poppy EnsPla51 p, n 41770
                      eudicotyledons (eudicots)
                        Superasterids
                           Caryophyllales
                              Cactineae
                              Chenopodiaceae Beta-vulgaris Beet EnsPla50 p, n 26521
                           Ericales Actinidia-chinensis Golden kiwifruit EnsPla53 p, n 33043
                           Asterids          
                              Lamiids          
                                Gentianales Coffea-canephora Coffee EnsPla50 p, n 25574
                                Solanales          
                                   Solanaceae          
                                     Nicotianoideae Nicotiana-attenuata Tobacco EnsPla50 p, n 33320
                                     Solanoideae          
                                        Capsiceae Capsicum-annuum Pepper EnsPla50 p, n 35845
                                        Solaneae   Solanum-melongena Eggplant  
  Solanum-tuberosum Potato EnsPla50 p, n 39021
  Solanum-lycopersicum Tomato EnsPla50 p, n 34429
                        Superrosids
                           Vitales Vitis-vinifera Grape EnsPla50 p, n 29927
                           Rosids          
                              Fabids            
                                Malpighiales Populus-trichocarpa Black cottonwood EnsPla50 p, n 41335
                                Fabales
                                   genistoids Lupinus-angustifolius Narrow-leaved blue lupine EnsPla51 p, n 33074
                                   NPAAA clade            
                                     Hologalegina Trifolium-pratense Red clover EnsPla51 p, n 39917
  Medicago-truncatula Barrel medic EnsPla51 p, n 50444
                                     Phaseoleae Phaseolus-vulgaris Common bean EnsPla51 p, n 28134
  Glycine-max Soybean EnsPla51 p, n 55897
  Vigna-radiata Mung bean EnsPla51 p, n 22368
  Vigna-angularis Adzuki bean EnsPla51 p, n 33860
                                Cucurbitales Cucumis-sativus Cucumber EnsPla50 p, n 23780
                                Rosales
                                   Rosaceae
                                     Rosoideae Rosa-chinensis China rose EnsPla58
                                     Amygdaloideae
                                        Maleae Malus-domestica Apple EnsPla58
                                        Amygdaleae Prunus-persica Peach EnsPla58
                              Malvids
                                Myrtales Eucalyptus-grandis Flooded gum EnsPla58 p, n 36779
  Corymbia-citriodora Lemon-scented gum EnsPla58
                                Sapindales
                                   Hippocastanoideae Acer-palmatum Japanese maple  
                                   Anacardiaceae Pistacia-vera Pistachio EnsPla58 p, n 31784
                                   Rutaceae Citrus-sinensis Sweet orange Ref220609 p, n 24456
                                Malvales
                                   Byttnerioideae Theobroma-cacao Cacao EnsPla50 p, n 29188
                                   Malvoideae Gossypium-raimondii Cotton plant EnsPla58 p, n 38208
                                   Bombacoideae Adansonia-digitata Baobab  
                                Brassicales
                                   Caricaceae Carica-papaya Papaya RefSeq240229 p, n 18003
                                   Brassicaceae
                                     Arabideae Arabis-alpina Gray rockcress EnsPla58 p, n 21609
                                     Eutremeae Eutrema-salsugineum Saltwater cress EnsPla58 p, n 26528
                                     Brassiceae Raphanus-sativus Radish RefSeq240229 p, n 51318
  Brassica-rapa Field mustard EnsPla58 p, n 41018
                                     Camelineae Camelina-sativa False flax EnsPla54 p, n 89275
  Arabidopsis-lyrata Lyrate rockcress EnsPla58 p, n 32667
  Arabidopsis-thaliana Thale cress EnsPla42 p, n 27628
  jinoueATg.ecc.u-tokyo.ac.jp