ORTHOSCOPE v1.5.1 - AORI
Gene tree and orthogroup estimation using a species tree (< 5 min as default). 1 January 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
 
  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
    Embryophyta (land plants)
          Bryophyta (mosses)
             Bryophytina Physcomitrella-patens Spreading earthmoss EnsPla50 p, n 32234
          Marchantiophyta Marchantia-polymorpha common liverwort EnsPla51 p, n 19287
          Tracheophyta (vascular plants)
             Lycopodiopsida Selaginella-moellendorffii Club mosses EnsPla50 p, n 34799
             Euphyllophyta          
                Polypodiopsida (ferns)
                Spermatophyta (seed plants)
                   Acrogymnospermae (gymnosperms)
                   Magnoliopsida (Angiospermae, flowering plants)
                      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 (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 Triticum-aestivum Bread wheat EnsPla50 p, n 107545
                                        Oryzoideae   Oryza-sativa-Indica Long-grained rice Comming soon xxxx
  Oryza-sativa-Japonica Japanese rice EnsPla50 p, n 35775
                         eudicotyledons (eudicots)
                            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            
                                  Sapindales
                                     Hippocastanoideae
                                     Anacardiaceae
                                     Rutaceae   Citrus-clementina Clementine mandarin Comming soon xxxx
                                  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

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