ORTHOSCOPE v1.5.5: Plants
Gene tree and orthogroup estimation using a species tree (< 5 min as default). 2 Oct. 2024
Instructions, Species tree Support: Safari, Firefox, Chrome yuraio
NEWS A script for genome wide data, ORTHOSCOPE*, has bee published.
Focal group    
Actinopterygians Mammals Vertebrates Deuterostomes Protostomes Acropora Plants
Status
Ready.
 
Mode Estimating gene tree Comparing gene and species trees Downloading 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
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
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
   Phaeophyceae (brown algae)
      Ectocarpales Nemacystus-decipiens Ito mozuku OIST
  Cladosiphon-okamuranus Okinawa mozuku OIST
   Alveolata
      Symbiodiniaceae Durusdinium-sp Dinoflagellate algae OIST
  Symbiodinium-minutum Dinoflagellate algae OIST
  Symbiodinium-microadriaticum Dinoflagellate algae EnsProt44 p, n 43403
Rhodophyta (red algae)
   Florideophyceae Chondrus-crispus Irish moss EnsPla58
   Bangiophyceae
      Galdieriales Galdieria-sulphuraria Red algae EnsPla58
      Cyanidiales Cyanidioschyzon-merolae Red algae EnsPla58
Haptophyta Emiliania-huxleyi Coccolithophore EnsProt44 p, n 38544
 
Viridiplantae (green plants)
 Chlorophyta (green algae)
    Mamiellophyceae Ostreococcus-lucimarinus Green algae EnsPla58
    Chlorophyceae Chlamydomonas-reinhardtii Chlamydomonas EnsPla58
    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