ORTHOSCOPE v1.5.1 - AORI
Gene tree and orthogroup estimation using a species tree (< 5 min as default). 14 August 2021
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
 
  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%

             
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
  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          
 Chlorophyta Caulerpa-lentillifera Siphonous green alga OIST-S p, n 9311
 Streptophyta          
    Charophyceae Chara-braunii Braun's stonewort EnsPla51 p, n 34718
       Embryophyta          
          Bryophyta Physcomitrella-patens Spreading earthmoss EnsPla50 p, n 32234
          Marchantiophyta Marchantia-polymorpha common liverwort EnsPla51 p, n 19287
          Tracheophyta          
             Lycopodiopsida Selaginella-moellendorffii Club mosses EnsPla50 p, n 34799
             Euphyllophyta          
                Spermatophyta          
                   Acrogymnospermae          
                   Magnoliopsida          
                      Nymphaeales Nymphaea-colorata Water lily EnsPla51 p, n 35831
                      Amborellales Amborella-trichopoda Amborella EnsPla51 p, n 27313
                      Mesangiospermae          
                         Ranunculales Papaver-somniferum Opium poppy EnsPla51 p, n 41770
                         Liliopsida          
                            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 Triticum-aestivum Bread wheat EnsPla50 p, n 107545
                                        Oryzoideae Oryza-sativa Rice EnsPla50 p, n 35775
                         eudicotyledons          
                            Caryophyllales Beta-vulgaris Beet EnsPla50 p, n 26521
                            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
                            rosids          
                               rosids incertae sedis Vitis-vinifera Grape EnsPla50 p, n 29927
                               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            
                                  Malvales Theobroma-cacao Cacao EnsPla50 p, n 29188
                                  Brassicales          
                                     Caricaceae   Carica-papaya Papaya xxxx p,n xxxx
                                     Brassicaceae Arabidopsis-thaliana Thale cress EnsPla42 p, n 27628

  jun.inoueAToist.jp