ORTHOSCOPE v1.5.2: Plants
Gene tree and orthogroup estimation using a species tree (< 5 min as default). 8 Mar. 2024
Instructions, Species tree Support: Safari(except for v14), Firefox, Chrome osaka

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

Query sequences (fasta format): DNA  Amino acid  Example fasta file: DNA, Amino acid
 
  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.
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 Transparent sea squirt Ens91 p, n 16671
  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 (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