ORTHOSCOPE v1.5.2 - yurai
Gene tree and orthogroup estimation using a species tree (< 5 min as default). 1 Sept. 2022
Instructions, Species tree Support: Safari(except for v14), Firefox, Chrome

Focal group    
Actinopterygii Mammalia Vertebrata Deuterostomia Protostomia Acropora Plants

Status
Ready.
 

Mode Estimating gene tree Comparing gene and species trees

Upload file Sequences (fasta): 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 Symbiodinium-microadriaticum Dinoflagellate EnsProt44 p, n 43403
Haptophyta Emiliania-huxleyi Coccolithophore EnsProt44 p, n 38544
           
Viridiplantae (green plants)
 Chlorophyta (green algae)
    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 Azolla-filiculoides Mosquito fern FernBase p, n 20203
  Salvinia-cucullata Asian watermoss FernBase p, n 19779
                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
                            Cupressaceae Taxus-baccata English yew p, n 32062
                            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 (Angiospermae, 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          
                                        Andropogoneae Sorghum-bicolor Sorghum EnsPla50 p, n 34118
                                        Panicodae Setaria-italica Foxtail millet EnsPla51 p, n 35831
                                     BOP clade          
                                        Pooideae            
                                           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-sativa-Indica Long-grained rice Comming soon xxxx
  Oryza-sativa-Japonica Japanese rice EnsPla50 p, n 35775
                         Ranunculales Papaver-somniferum Opium poppy EnsPla51 p, n 41770
                         eudicotyledons (eudicots)
                            Superasterids
                               Caryophyllales Beta-vulgaris Beet EnsPla50 p, n 26521
                               Ericales Actinidia-chinensis Golden kiwifruit EnsPla53
                               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 xxxx p,n xxxx
  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
                                     Cucurbitales Cucumis-sativus Cucumber EnsPla50 p, n 23780
                                     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
                                  Malvids            
                                     Sapindales
                                        Hippocastanoideae
                                        Anacardiaceae
                                        Rutaceae Citrus-sinensis Sweet orange Ref220609 p, n 24456
                                     Malvales Theobroma-cacao Cacao EnsPla50 p, n 29188
                                     Brassicales            
                                        Caricaceae   Carica-papaya Papaya RefSeq220610 p,n xxxx
                                        Brassicaceae            
                                           Camelineae Camelina-sativa False flax EnsPla54 p, n 89275
  Arabidopsis-thaliana Thale cress EnsPla42 p, n 27628

  jinoueATg.ecc.u-tokyo.ac.jp