ORTHOSCOPE: deuterostome orthogroup
Gene tree and orthogroup estimation using a species tree (< 5 min with 20-30 spp).
Instruction Support: Safari(latest), Firefox, Chrome Ver.1.0

Analysis group    
Actinopterygii Vertebrata Deuterostomia Protostomia

Status
Ready.
 

Mode Tree search only Search/rearrangement

Upload file Coding or amino acid sequence set
(fasta)
Species tree
(newick)
 
  Amino acid  DNA  Example 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 hits to report per genome 3   5   10
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    
Non bilaterians        
Fungi Saccharomyces cerevisiae Baker's yeast Ens92
  Saccharomyces cerevisiae 1 Baker's yeast RefSeq90
Ichthyosporea Sphaeroforma arctica RefSeq90
  Capsaspora owczarzaki RefSeq90
Salpingoecidae Salpingoeca rosetta RefSeq90
  Monosiga brevicollis RefSeq90
Ctenophora Mnemiopsis leidyi American comb jelly EnsMet38
Porifera Amphimedon queenslandica Sponge EnsMet38
Placozoa Trichoplax adhaerens EnsMet38
Cnidaria        
  Myxozoa Thelohanellus kitauei Myxosporean EnsMet38
  Hydrozoa Hydra vulgaris Hydra NCBI
  Actiniaria Exaiptasia pallida Sea anemone EnsMet38
  Nematostella vectensis Starlet sea anemone EnsMet38
  Nematostella vectensis 1 Starlet sea anemone RefSeq89
  Orbicella faveolata Mountainous star coral NCBI
  Stylophora pistillata Hood coral NCBI
  Acropora digitifera Acroporid coral NCBI
Bilateria        
Protostomia        
Spiralia        
  Rotifera Adineta vaga Rotifer EnsMet39
  Platyhelminthes Schistosoma mansoni Blood fluke EnsMet40
  Annelida Capitella teleta Polychaete worm EnsMet39
  Helobdella robusta Californian leech EnsMet39
  Nemertea Notospermus geniculatus Ribbon worm OIST-S
  Phoronid Phoronis australis horseshoe worm OIST-S
  Brachiopoda Lingula anatina Lamp shell EnsMet38
  Cephalopoda Octopus bimaculoides California two-spotted octopus EnsMet38
  Gastropoda Lottia gigantea Giant owl limpet EnsMet38
  Biomphalaria glabrata Bloodfluke planorb NCBI
  Aplysia californica California sea hare NCBI
  Bivalvia Crassostrea virginica Eastern oyster NCBI
  Crassostrea gigas Pacific oyster EnsMet40
  Mizuhopecten yessoensis Ezo giant scallop NCBI
  Pinctada fucata Pearl oyster OIST-S
Ecdysozoa        
  Priapulida Priapulus caudatus Priapulid worm NCBI
  Nematoda Trichinella spiralis Trichina worm EnsMet39
  Strongyloides ratti Parasitic roundworm EnsMet39
  Onchocerca volvulus EnsMet39
  Loa loa Eye worm EnsMet39
  Brugia malayi Filarial nematode worm EnsMet39
  Pristionchus pacificus Parasitic nematode EnsMet39
  Caenorhabditis japonica Nematode worm EnsMet39
  Caenorhabditis brenneri Nematode worm EnsMet39
  Caenorhabditis remanei Nematode worm EnsMet39
  Caenorhabditis briggsae Nematode worm EnsMet39
  Caenorhabditis elegans Nematode worm EnsMet38
  Caenorhabditis elegans 1 Nematode worm RefSeq89
  Chelicerata Limulus polyphemus Atlantic horseshoe crab NCBI
  Sarcoptes scabiei Itch mite EnsMet38
  Tetranychus urticae Red spider mite EnsMet38
  Ixodes scapularis Blacklegged tick EnsMet38
  Centruroides sculpturatus Bark scorpion NCBI
  Parasteatoda tepidariorum House spider NCBI
  Stegodyphus mimosarum African social velvet spider EnsMet38
  Myriapoda Strigamia maritima European centipede EnsMet38
  Crustacea Hyalella azteca Amphipod NCBI
  Eurytemora affinis Copepod NCBI
  Lepeophtheirus salmonis Salmon louse EnsMet39
  Daphnia magna EnsMet39
  Daphnia pulex Water flea EnsMet39
  Hexapoda        
    Paraneoptera Pediculus humanus Human lice EnsMet38
    Dictyoptera Zootermopsis nevadensis Dampwood termite EnsMet39
  Cryptotermes secundus Drywood termite NCBI
    Hemiptera Rhodnius prolixus Triatomid bug EnsMet39
  Acyrthosiphon pisum Pea aphid EnsMet39
    Hymenoptera Nasonia vitripennis Parasitic wasp EnsMet39
  Atta cephalotes Leafcutter ant NCBI
  Solenopsis invicta Imported red fire ant NCBI
  Apis mellifera European honey bee EnsMet39
  Bombus impatiens Bumblebee EnsMet39
  Bombus terrestris Large earth bumblebee EnsMet39
    Coleoptera Tribolium castaneum Rust-red flour beetle EnsMet39
  Anoplophora glabripennis Asian long-horn beetle EnsMet39
  Dendroctonus ponderosae Mountain pine beetle EnsMet39
    Lepidoptera Bombyx mori Silkworm EnsMet38
  Heliconius melpomene Postman butterfly EnsMet39
  Danaus plexippus American monarch EnsMet39
  Melitaea cinxia Glanville fritillary EnsMet39
    Diptera Belgica antarctica Antarctic midge EnsMet39
  Anopheles darlingi African malaria mosquito EnsMet39
  Culex quinquefasciatus Southern house mosquito EnsMet39
  Aedes aegypti Yellow fever mosquito EnsMet39
  Mayetiola destructor Hessian fly EnsMet39
  Megaselia scalaris Humpbacked fly EnsMet39
  Teleopsis dalmanni Malaysian stalk-eyed fly EnsMet39
  Lucilia cuprina Australian sheep blowfly NCBI
  Drosophila grimshawi Fruit fly EnsMet39
  Drosophila mojavensis Fruit fly EnsMet39
  Drosophila virilis Fruit fly EnsMet39
  Drosophila willistoni Fruit fly EnsMet39
  Drosophila pseudoobscura Fruit fly EnsMet39
  Drosophila persimilis Fruit fly EnsMet39
  Drosophila ananassae Fruit fly EnsMet39
  Drosophila yakuba Fruit fly EnsMet39
  Drosophila erecta Fruit fly EnsMet39
  Drosophila simulans Fruit fly EnsMet39
  Drosophila sechellia Fruit fly EnsMet39
  Drosophila melanogaster Fruit fly EnsMet38
  Drosophila melanogaster 1 Fruit fly RefSeq89
Deuterostomia      
Hemichordata Saccoglossus kowalevskii Helical acorn worm OIST-R
  Saccoglossus kowalevskii 1 Helical acorn worm RefSeq89
  Ptychodera flava Yellow acorn worm OIST-S
Echinodermata Strongylocentrotus purpuratus Purple urchin EnsMet38
  Strongylocentrotus purpuratus 1 Purple urchin RefSeq89
  Acanthaster planci Crown-of-thorns starfish (Okinawa) OIST-S
  Acanthaster planci 1 Crown-of-thorns starfish (Okinawa) RefSeq89
  Acanthaster planci GBR Crown-of-thorns starfish (Great Barrier Reef) OIST-S
Cephalochordata Branchiostoma floridae Florida lancelet JGI
  Branchiostoma floridae 1 Florida lancelet RefSeq89
  Branchiostoma belcheri Belcher's lancelet LanceletDB
  Branchiostoma belcheri 1 Belcher's lancelet RefSeq89
Urochordata Oikopleura dioica Pelagic tunicate OikoBase
  Botryllus schlosseri Golden star tunicate Stanford
  Ciona savignyi Pacific transparent sea squirt Ens91
  Ciona intestinalis Transparent sea squirt Ens91
  Ciona intestinalis 1 Transparent sea squirt RefSeq89
Vertebrata  
 Cyclostomata Petromyzon marinus Sea lamprey PMZv3.1
 Chondrichthyes Callorhinchus milii Elephant shark RefSeq89
  Rhincodon typus Whale shark RefSeq89
 Actinopterygii        
 Lepisosteidae Lepisosteus oculatus Spotted gar Ens91
  Lepisosteus oculatus 1 Spotted gar RefSeq89
 Teleostei       Ens91
 Osteoglossomorpha Scleropages formosus Asian arowana NCBI
  Paramormyrops kingsleyae Elephantfish NCBI
 Clupeocephala        
  Otomorpha Clupea harengus Atlantic herring NCBI
  Ictalurus punctatus Channel catfish NCBI
  Astyanax mexicanus Blind cave fish Ens91
  Pygocentrus nattereri Red piranha NCBI
  Danio rerio Zebrafish Ens91
  Danio rerio 1 Zebrafish RefSeq89
  Sinocyclocheilus grahami Golden-line barbel NCBI
  Cyprinus carpio Common carp NCBI
  Protacanthopterygii Esox lucius Northern pike NCBI
  Salmo salar Atlantic salmon NCBI
  Salvelinus alpinus Arctic char NCBI
  Oncorhynchus mykiss Rainbow trout NCBI
  Oncorhynchus tshawytscha Chinook salmon NCBI
  Oncorhynchus kisutch Coho salmon NCBI
  Acanthomorphata        
   Gadiformes Gadus morhua Atlantic cod Ens91
   Gasterosteiformes Gasterosteus aculeatus Three spined stickleback Ens91
   Notothenioidei Notothenia coriiceps Yellowbelly rockcod NCBI
   Sciaenidae Larimichthys crocea Croceine croaker NCBI
   Labridae Labrus bergylta Ballan wrasse NCBI
   Tetraodontiformes Tetraodon nigroviridis Spotted green pufferfish Ens91
  Takifugu rubripes Torafugu Ens91
  Takifugu rubripes 1 Torafugu RefSeq89
   Pleuronectiformes Cynoglossus semilaevis Half-smooth tongue sole NCBI
  Paralichthys olivaceus Japanese flounder NCBI
   Centropomidae Lates calcarifer Barramundi perch NCBI
   Carangiformes Seriola lalandi-dorsalis Yellowtail amberjack NCBI
  Seriola dumerili Greater amberjack NCBI
   Pomacentridae Stegastes partitus Bicolor damselfish NCBI
  Amphiprion ocellaris Clown anemonefish NCBI
  Acanthochromis polyacanthus Spiny chromis NCBI
   Cichlidae Oreochromis niloticus Nile tilapia Ens91
  Neolamprologus brichardi Yretail cichlid NCBI
  Pundamilia nyererei Python island NCBI
  Maylandia zebra Zebra mbuna NCBI
  Haplochromis burtoni Burton's mouthbrooder NCBI
   Syngnathiformes Hippocampus comes Tiger tail seahorse NCBI
   Gobiiformes Boleophthalmus pectinirostris Great blue-spotted mudskipper NCBI
   Synbranchiformes Monopterus albus Swamp eel NCBI
   Atherinomorpha Nothobranchius furzeri Turquoise killifish NCBI
  Austrofundulus limnaeus NCBI
  Cyprinodon variegatus Sheepshead minnow NCBI
  Fundulus heteroclitus Atlantic killifish (Mummichog) NCBI
  Xiphophorus maculatus Southern platyfish Ens91
  Poecilia formosa Amazon molly Ens91
  Poecilia reticulata Guppy NCBI
  Oryzias melastigma Indian medaka Ens91
  Oryzias latipes Medaka Ens91
  Oryzias latipes 1 Medaka RefSeq89
 Sarcopterygii        
   Latimeria Latimeria chalumnae Coelacanth Ens91
  Latimeria chalumnae 1 Coelacanth RefSeq89
   Amphibia Nanorana parkeri RefSeq90
  Xenopus tropicalis Western clawed frog Ens91
  Xenopus tropicalis 1 Western clawed frog NCBI
  Xenopus laevis Clawed frog NCBI
  Xenopus laevis 1 Clawed frog RefSeq89
   Lepidosauria Gekko japonicus Schlegel's Japanese gecko NCBI
  Python bivittatus Burmese python NCBI
  Thamnophis sirtalis Common garter snake NCBI
  Protobothrops mucrosquamatus Taiwan habu NCBI
  Protobothrops flavoviridis Habu OIST-S
  Pogona vitticeps Central bearded dragon NCBI
  Anolis carolinensis Green anole Ens91
  Anolis carolinensis 1 Green anole RefSeq89
   Testudines Pelodiscus sinensis Chinese soft-shelled turtle Ens91
  Chelonia mydas Green seaturtle NCBI
  Terrapene mexicana Mexican box turtle RefSeq89
  Chrysemys picta Painted turtle NCBI
   Crocodylia Crocodylus porosus Estuarine crocodile RefSeq89
  Gavialis gangeticus True gharial RefSeq89
  Alligator mississippiensis American alligator NCBI
  Alligator sinensis Chinese alligator NCBI
   Aves Ficedula albicollis Collared flycatcher Ens91
  Anas platyrhynchos Mallard Ens91
  Taeniopygia guttata Zebra finch Ens91
  Meleagris gallopavo Turkey Ens91
  Gallus gallus Chicken Ens91
  Gallus gallus 1 Chicken RefSeq90
   Mammalia        
    Ornithorhynchus Ornithorhynchus anatinus Platypus Ens92
    Marsupialia Monodelphis domestica Gray short-tailed opossum Ens92
  Sarcophilus harrisii Tasmanian devil Ens92
  Notamacropus eugenii Tammar wallaby Ens92
    Afrotheria Orycteropus afer Aardvark NCBI
  Echinops telfairi Madagascar hedgehog Ens92
  Loxodonta africana African elephant Ens92
  Trichechus manatus Florida manatee NCBI
  Procavia capensis Cape rock hyrax Ens92
    Xenarthra Dasypus novemcinctus Nine-banded armadillo Ens92
  Choloepus hoffmanni Hoffmann's two-fingered sloth Ens92
    Laurasiatheria Erinaceus europaeus Western European hedgehog Ens92
  Sorex araneus European shrew Ens92
  Pteropus vampyrus Large flying fox Ens92
  Myotis lucifugus Little brown bat Ens92
  Equus caballus Horse Ens92
  Ceratotherium simum White rhinoceros NCBI
  Manis javanica Malayan pangolin NCBI
  Felis catus Domestic cat Ens92
  Canis familiaris Dog Ens92
  Mustela putorius-furo European polecat (Ferret) Ens92
  Leptonychotes weddellii Weddell seal NCBI
  Ailuropoda melanoleuca Giant panda Ens92
  Ursus maritimus Polar bear NCBI
  Camelus bactrianus Bactrian camel NCBI
  Vicugna pacos Alpaca Ens92
  Sus scrofa Pig Ens92
  Sus scrofa 1 Pig NCBI
  Odocoileus virginianus White-tailed deer NCBI
  Bubalus bubalis Water buffalo NCBI
  Bison bison American bison NCBI
  Bos taurus Domestic cow Ens92
  Bos taurus 1 Domestic cow RefSeq89
  Ovis aries Domestic sheep Ens92
  Capra hircus Domestic goat Ens92
  Balaenoptera acutorostrata Minke whale NCBI
  Physeter catodon Sperm whale NCBI
  Lipotes vexillifer Yangtze River dolphin NCBI
  Tursiops truncatus Bottlenose-dolphin Ens92
  Orcinus orca Killer whale NCBI
    Tupaia Tupaia belangeri Common tree shrew Ens92
    Glires Oryctolagus cuniculus Domestic rabbit Ens92
  Ochotona princeps Southern American pika Ens92
  Ictidomys tridecemlineatus Thirteen-lined ground squirrel Ens92
  Fukomys damarensis Damara mole rat Ens92
  Heterocephalus glaber-female Naked mole rat Ens92
  Octodon degus Degu Ens92
  Chinchilla lanigera Long-tailed chinchilla Ens92
  Cavia porcellus Guinea pig Ens92
  Cavia aperea Brazilian guinea pig Ens92
  Dipodomys ordii Ord's kangaroo rat Ens92
  Jaculus jaculus Egyptian jerboa Ens92
  Nannospalax galili Upper Galilee mountains blind mole rat Ens92
  Peromyscus maniculatus bairdii North American deer mouse Ens92
  Cricetulus griseus CHOK1GS-HDv1 Chinese hamster Ens92
  Rattus norvegicus Norway rat Ens92
  Rattus norvegicus 1 Norway rat RefSeq89
  Mus pahari Gairdner's shrew-mouse Ens92
  Mus spretus Algerian mouse Ens92
  Mus musculus House mouse Ens91
  Mus musculus 1 House mouse NCBI
    Primates Otolemur garnettii Small-eared galago Ens92
  Microcebus murinus Gray mouse lemur NCBI
  Propithecus coquereli Propithecus coquereli Ens92
  Carlito syrichta Philippine tarsier Ens92
  Aotus nancymaae Ma's night monkey Ens92
  Callithrix jacchus Common marmoset Ens92
  Cebus capucinus White-faced capuchin Ens92
  Saimiri boliviensis boliviensis Bolivian squirrel monkey Ens92
  Colobus angolensis palliatus Peters' Angolan colobus Ens91
  Rhinopithecus roxellana Golden snub-nosed monkey Ens91
  Rhinopithecus bieti Black snub-nosed monkey Ens91
  Chlorocebus sabaeus Green monkey Ens91
  Papio anubis Kenya baboon Ens91
  Cercocebus atys Sooty mangabey Ens91
  Mandrillus leucophaeus Drill Ens91
  Macaca nemestrina Pigtail macaqu Ens91
  Macaca fascicularis Crab eating macaque Ens91
  Macaca mulatta Rhesus macaque Ens91
  Nomascus leucogenys White-cheeked Gibbon Ens92
  Pongo abelii Orangutan Ens92
  Gorilla gorilla Western gorilla Ens92
  Pan troglodytes Chimpanzee Ens92
  Pan paniscus Pygmy chimpanzee Ens92
  Homo sapiens Human Ens91
  Homo sapiens 1 Human RefSeq89

Last modified: 14 Nov. 2018   jun.inoueAToist.jp