ORTHOSCOPE v1.5.1 - AORI
Gene tree and orthogroup estimation using a species tree (< 5 min as default). 7 Apr. 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%

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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          
 Embryophyta          
    Bryophyta Physcomitrella patens Spreading earthmoss EnsPla50 p, n 32234
    Tracheophyta          
       Lycopodiopsida Selaginella moellendorffii Club mosses EnsPla50 p, n 34799
       Euphyllophyta          
          Spermatophyta          
             Magnoliopsida          
                Mesangiospermae          
                   Liliopsida          
                      Poaceae          
                         PACMAD clade Sorghum bicolor Sorghum EnsPla50 p, n 34118
                         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
                      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
                         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
                      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

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