ORTHOSCOPE v1.5.1
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 Mirror: AORI

Focal group    
Actinopterygii Mammalia Vertebrata Deuterostomia Protostomia Acropora Plants

Status
Ready.
 

Mode Tree Search Only
(Estimating gene tree)
Search/Rearrangement
(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
BLAST 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
Non metazoans          
Bacteria          
 Cyanobacteria Prochlorococcus-marinus Cyanobacteria (MIT 9211) EnsBac42 p, n 1855
 Actinobacteria Corynebacterium-efficiens C.efficiens YS-314 EnsBac42 p, n 2998
  Streptomyces-coelicolor S.coelicolor A3(2) EnsBac42 p, n 8154
Archaea Methanocaldococcus-jannaschii Euryarchaeotes EnsBac42 p, n 1770
           
Eukaryota          
Viridiplantae Arabidopsis-thaliana Thale cress EnsPla42 p, n 27628
Sar Symbiodinium-microadriaticum Dinoflagellate EnsProt44 p, n 43403
Haptophyta Emiliania-huxleyi Coccolithophore EnsProt44 p, n 38544
           
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          
Ctenophora Mnemiopsis-leidyi American comb jelly EnsMet38 p, n 16058
Porifera          
   Haplosclerida Amphimedon-queenslandica Sponge EnsMet38 p, n 43615
   Spongillida   Ephydatia-muelleri Sponge Coming soon Xxxx
Placozoa Trichoplax-adhaerens EnsMet38 p, n 11520
Cnidaria          
  Myxozoa Thelohanellus-kitauei Myxosporean EnsMet38 p, n 15020
  Hydrozoa Hydra-vulgaris Hydra RefSeq p, n 20042
  Cubozoa Morbakka-virulenta Cubozoan jellyfish OIST-S p, n 28983
  Scyphozoa Aurelia-aurita-P Moon jelly(Pacific) OIST-S p, n 37462
  Aurelia-aurita-A Moon jelly(Atlantic) OIST-S p, n 38008
  Anthozoa        
   Actiniaria        
    Aiptasiidae Exaiptasia-pallida Sea anemone NCBI p, n 22199
  Nematostella-vectensis Starlet sea anemone EnsMet38 p, n 24773
  Nematostella-vectensis-1 Starlet sea anemone RefSeq p, n 24773
   Corallimorpharia Amplexidiscus-fenestrafer Coral anemones REEF
GENOMICS
p, n 21372
  Discosoma-spp Coral anemones REEF
GENOMICS
p, n 23199
   Scleractinia        
    Merulinidae Orbicella-faveolata Mountainous star coral RefSeq p, n 25916
    Pocilloporidae Stylophora-pistillata Hood coral RefSeq p, n 24833
    Acroporidae Astreopora spp. Acroporid coral Shinzato20 p, n 28711
  Montipora-efflorescens Acroporid coral Shinzato20 p, n 21369
  Montipora-cactus Acroporid coral Shinzato20 p, n 21982
  Acropora-tenuis Acroporid coral Shinzato20 p, n 23118
  Acropora-yongei Acroporid coral Shinzato20 p, n 23500
  Acropora-gemmifera Acroporid coral Shinzato20 p, n 22247
  Acropora-florida Acroporid coral Shinzato20 p, n 23857
  Acropora-awi Acroporid coral Shinzato20 p, n 22653
  Acropora-intermedia Acroporid coral Shinzato20 p, n 23343
  Acropora-acuminata Acroporid coral Shinzato20 p, n 22306
  Acropora-nasta Acroporid coral Shinzato20 p, n 23319
  Acropora-microphthalma Acroporid coral Shinzato20 p, n 22618
  Acropora-digitifera Acroporid coral RefSeq p, n 26060
  Acropora-digitifera-1 Acroporid coral Shinzato20 p, n 22326
  Acropora-echinata Acroporid coral Shinzato20 p, n 43886
  Acropora-muricata Acroporid coral Shinzato20 p, n 23646
  Acropora-selago Acroporid coral Shinzato20 p, n 23115
  Acropora-hyacinthus Acroporid coral Shinzato20 p, n 23147
  Acropora-cytherea Acroporid coral Shinzato20 p, n 23363
           
Bilateria          
Deuterostomia          
Hemichordata Saccoglossus-kowalevskii Helical acorn worm OIST-R p, n 34239
  Saccoglossus-kowalevskii-1 Helical acorn worm RefSeq89 p, n 20922
  Ptychodera-flava Yellow acorn worm OIST-S p, n 34647
Echinodermata          
   Pelmatozoa Anneissia-japonica Crinoid RefSeq p, n 21084
   Eleutherozoa          
      Asteroidea Acanthaster-planci Crown-of-thorns starfish (Okinawa) OIST-S p, n 24323
  Acanthaster-planci-1 Crown-of-thorns starfish (Okinawa) RefSeq89 p, n 16468
  Acanthaster-planci-GBR Crown-of-thorns starfish (Great Barrier Reef) OIST-S p, n 24747
      Echinozoa          
         Holothuroidea   Apostichopus-japonicus Japanese sea cucumber Coming soon Xxxx
         Echinoidea   Lytechinus-variegatus Green sea urchin Coming soon Xxxx
  Strongylocentrotus-purpuratus Purple urchin EnsMet38 p, n 28842
  Strongylocentrotus-purpuratus-1 Purple urchin RefSeq89 p, n 27728
Cephalochordata Asymmetron-lucayanum-CH Lancelet TSA,CD-HIT p, n 60851
  Asymmetron-lucayanum Lancelet TSA p, n 104311
  Branchiostoma-belcheri Belcher's lancelet LanceletDB p, n 30392
  Branchiostoma-belcheri-1 Belcher's lancelet RefSeq89 p, n 23855
  Branchiostoma-lanceolatum Mediterranean amphioxus Amphiencode p, n 23586
  Branchiostoma-floridae Florida lancelet JGI p, n 21954
  Branchiostoma-floridae-1 Florida lancelet RefSeq89 p, n 28621
Urochordata          
 Appendicularia Oikopleura-dioica Pelagic tunicate OikoBase p, n 17212
 Thaliacea Salpa-thompsoni Salpa TSA p, n 76798
 Enterogona Ciona-savignyi Pacific transparent sea squirt Ens91 p, n 11616
  Ciona-savignyi-1 Pacific transparent sea squirt aNISEED p, n 20115
  Ciona-intestinalis Transparent sea squirt Ens91 p, n 16671
  Ciona-intestinalis-1 Transparent sea squirt RefSeq89 p, n 13520
 Molgulidae Molgula-occidentalis aNISEED p, n 33023
  Molgula-oculata Sea grape aNISEED p, n 16616
 Styelidae Botrylloides-leachii Leache's ascidian aNISEED p, n 15839
  Botryllus-schlosseri Golden star tunicate Stanford p, n 30910
Vertebrata          
 Cyclostomata          
    Myxiniformes Eptatretus-burgeri Inshore hagfish Ens94 p, n 16513
    Petromyzontiformes Petromyzon-marinus Sea lamprey PMZv3.1 p, n 20950
 Chondrichthyes Callorhinchus-milii Elephant shark RefSeq89 p, n 17847
    Batoidea Amblyraja-radiata-N Thorny skate RefSeq200601 p, n 18475
    Selachii          
       Carcharhiniformes Scyliorhinus-torazame Cloudy catshark Squalomix p, n 28051
       Orectolobiformes          
          Hemiscylliidae Chiloscyllium-punctatum Brownbanded bamboo shark Squalomix p, n 34038
          Orectolobiformes Rhincodon-typus Whale shark RefSeq89 p, n 21868
  Rhincodon-typus-R Whale shark Squalomix p, n 27005
 Actinopterygii          
    Polypteriformes Erpetoichthys-calabaricus Reedfish RefSeq100 p, n 22167
    Acipenseriformes Acipenser-ruthenus Sterlet RefSeq p, n 36020
    Lepisosteidae Lepisosteus-oculatus Spotted gar Ens91 p, n 18341
  Lepisosteus-oculatus-1 Spotted gar RefSeq89 p, n 18771
    Teleostei          
       Osteoglossomorpha Scleropages-formosus Asian arowana NCBI p, n 22740
  Paramormyrops-kingsleyae Elephantfish NCBI p, n 23862
       Elopomorpha Megalops-cyprinoides Indo-Pacific tarpon RefSeq201214 p, n 25343
  Anguilla-anguilla European eel RefSeq p, n 25890
       Clupeocephala          
          Otomorpha          
             Clupeiformes Denticeps-clupeoides Denticle herring RefSeq100 p, n 23474
  Clupea-harengus Atlantic herring NCBI p, n 23701
             Otophysi Danio-rerio Zebrafish Ens91 p, n 25902
  Danio-rerio-1 Zebrafish RefSeq89 p, n 26587
  Carassius-auratus Goldfish RefSeq100 p, n 53052
  Sinocyclocheilus-grahami Golden-line barbel NCBI p, n 45899
  Cyprinus-carpio Common carp NCBI p, n 49264
  Electrophorus-electricus Electric eel RefSeq100 p, n 22026
  Tachysurus-fulvidraco Yellow catfish RefSeq100 p, n 23554
  Pangasianodon-hypophthalmus Striped catfish RefSeq100 p, n 21654
  Ictalurus-punctatus Channel catfish NCBI p, n 22996
  Astyanax-mexicanus Blind cave fish Ens91 p, n 23042
  Pygocentrus-nattereri Red piranha NCBI p, n 25562
          Protacanthopterygii Esox-lucius Northern pike NCBI p, n 23798
  Salmo-salar Atlantic salmon NCBI p, n 48593
  Salvelinus-alpinus Arctic char NCBI p, n 36422
  Oncorhynchus-mykiss Rainbow trout NCBI p, n 42737
  Oncorhynchus-tshawytscha Chinook salmon NCBI p, n 42470
  Oncorhynchus-kisutch Coho salmon NCBI p, n 36349
          Acanthomorphata          
             Gadiformes Gadus-morhua Atlantic cod Ens91 p, n 20095
             Gasterosteiformes Gasterosteus-aculeatus Three spined stickleback Ens91 p, n 20787
             Notothenioidei Notothenia-coriiceps Yellowbelly rockcod NCBI p, n 24776
             Sciaenidae Larimichthys-crocea Croceine croaker NCBI p, n 24779
             Labridae Labrus-bergylta Ballan wrasse NCBI p, n 24748
             Tetraodontiformes Tetraodon-nigroviridis Spotted green pufferfish Ens91 p, n 19602
  Takifugu-rubripes Torafugu Ens91 p, n 18523
  Takifugu-rubripes-1 Torafugu RefSeq p, n 21323
             Pleuronectiformes Cynoglossus-semilaevis Half-smooth tongue sole NCBI p, n 21382
  Paralichthys-olivaceus Japanese flounder NCBI p, n 23113
             Centropomidae Lates-calcarifer Barramundi perch NCBI p, n 25329
             Carangiformes Seriola-lalandi-dorsalis Yellowtail amberjack NCBI p, n 25789
  Seriola-dumerili Greater amberjack NCBI p, n 22005
             Pomacentridae Stegastes-partitus Bicolor damselfish NCBI p, n 22589
  Amphiprion-ocellaris Clown anemonefish NCBI p, n 23512
  Acanthochromis-polyacanthus Spiny chromis NCBI p, n 24580
             Cichlidae Oreochromis-niloticus Nile tilapia Ens91 p, n 21437
  Neolamprologus-brichardi Yretail cichlid NCBI p, n 22678
  Pundamilia-nyererei Python island NCBI p, n 22890
  Maylandia-zebra Zebra mbuna NCBI p, n 25885
  Haplochromis-burtoni Burton's mouthbrooder NCBI p, n 24002
             Syngnathiformes Hippocampus-comes Tiger tail seahorse RefSeq p, n 21175
             Gobiiformes Boleophthalmus-pectinirostris Great blue-spotted mudskipper NCBI p, n 21391
             Synbranchiformes Monopterus-albus Swamp eel NCBI p, n 21343
             Atherinomorpha Nothobranchius-furzeri Turquoise killifish NCBI p, n 22194
  Austrofundulus-limnaeus NCBI p, n 23805
  Cyprinodon-variegatus Sheepshead minnow NCBI p, n 23264
  Fundulus-heteroclitus Atlantic killifish (Mummichog) NCBI p, n 23511
  Xiphophorus-maculatus Southern platyfish Ens91 p, n 20379
  Poecilia-formosa Amazon molly Ens91 p, n 23615
  Poecilia-reticulata Guppy NCBI p, n 22829
  Oryzias-melastigma Indian medaka Ens91 p, n 23157
  Oryzias-latipes Medaka Ens91 p, n 19699
  Oryzias-latipes-1 Medaka RefSeq89 p, n 22058
 Sarcopterygii          
   Latimeria Latimeria-chalumnae Coelacanth Ens91 p, n 19569
  Latimeria-chalumnae-1 Coelacanth RefSeq p, n 20932
   Amphibia          
     Gymnophiona Rhinatrema-bivittatum Two-lined caecilian RefSeq100 p, n 21539
  Caecilia-tentaculata Guayaquil caecilian TSA p, n 93723
  Typhlonectes-compressicauda Cayenne caecilian TSA p, n 85502
  Microcaecilia-dermatophaga Tiny white caecilian TSA p, n 62376
  Microcaecilia-unicolor Tiny Cayenne caecilian RefSeq100 p, n 20854
     Caudata Tylototriton-wenxianensis Wenxian knobby newt TSA p, n 125603
     Anura Nanorana-parkeri High Himalaya frog RefSeq90 p, n 18945
  Xenopus-tropicalis Western clawed frog Ens91 p, n 18442
  Xenopus-tropicalis-1 Western clawed frog NCBI p, n 21364
  Xenopus-laevis Clawed frog NCBI p, n 31332
  Xenopus-laevis-1 Clawed frog RefSeq89 p, n 31332
  Lepidosauria          
     Sphenodontia Sphenodon-punctatus Tuatara Ens98 p, n 17648
     Squamata          
        Gekkonidae Gekko-japonicus Schlegel's Japanese gecko RefSeq p, n 19463
        Unidentata          
           Laterata          
              Lacertidae Podarcis-muralis Common wall lizard RefSeq p, n 21243
  Salvator-merianae Argentine black and white tegu Ens98 p, n 19342
           Toxicofera          
              Iguania Pogona-vitticeps Central bearded dragon NCBI p, n 18891
  Anolis-carolinensis Green anole Ens91 p, n 18595
  Anolis-carolinensis-1 Green anole RefSeq89 p, n 19352
              Serpentes          
                 Henophidia Python-bivittatus Burmese python RefSeq p, n 19793
                 Colubroidea          
                    Viperidae Protobothrops-mucrosquamatus Taiwan habu NCBI p, n 20001
  Protobothrops-flavoviridis Habu OIST-S p, n 25134
                    Colubridae Pantherophis-guttatus Corn snake RefSeq202024 p, n 19907
  Thamnophis-elegans Western terrestrial garter snake RefSeq202024 p, n 18900
  Thamnophis-sirtalis Common garter snake RefSeq p, n 18565
                    Elapidae          
                       Elapinae Naja-naja Indian cobra Ens102 p, n 18011
                       Laticaudinae Laticauda-laticaudata Blue-ringed sea krait Ens102 p, n 17627
                       Acanthophiinae Pseudonaja-textilis Eastern brown snake RefSeq100 p, n 19356
  Notechis-scutatus Mainland tiger snake RefSeq100 p, n 19768
  Archosauria          
   Testudines          
      Trionychidae Pelodiscus-sinensis Chinese soft-shelled turtle Ens91 p, n 18189
      Durocryptodira Chelonia-mydas Green seaturtle RefSeq p, n 17747
  Chelonoidis-abingdonii Abingdon island giant tortoise Ens98 p, n 20204
  Terrapene-mexicana Mexican box turtle RefSeq89 p, n 21270
  Chrysemys-picta Painted turtle NCBI p, n 21077
   Crocodylia Crocodylus-porosus Estuarine crocodile RefSeq89 p, n 14704
  Gavialis-gangeticus True gharial RefSeq89 p, n 14302
  Alligator-mississippiensis American alligator NCBI p, n 18942
  Alligator-sinensis Chinese alligator NCBI p, n 18583
   Aves          
     Palaeognathae          
        Struthioniformes Struthio-camelus African ostrich RefSeq90 p, n 14577
        Tinamiformes Tinamus-guttatus White-throated tinamou RefSeq90 p, n 15723
  Nothoprocta-perdicaria Chilean tinamou RefSeq90 p, n 15074
        Apterygiformes Apteryx-rowi Okarito brown kiwi RefSeq90 p, n 15883
  Apteryx-australis Brown kiwi RefSeq90 p, n 16251
        Casuariiformes Dromaius-novaehollandiae Emu RefSeq90 p, n 15541
     Neognathae          
        Galloanseres          
           Anseriformes Anser-cygnoides Swan goose RefSeq90 p, n 14696
  Anas-platyrhynchos Mallard duck Ens91 p, n 15634
  Anas-platyrhynchos-1 Mallard duck RefSeq90 p, n 14939
           Galliformes Meleagris-gallopavo Turkey Ens91 p, n 14123
  Meleagris-gallopavo-1 Turkey RefSeq90 p, n 18465
  Coturnix-japonica Japanese quail RefSeq90 p, n 16024
  Gallus-gallus-E102 Chicken Ens102 p, n 16878
  Gallus-gallus-E99 Chicken Ens99 p, n 16878
  Gallus-gallus Chicken Ens91 p, n 18346
  Gallus-gallus-1 Chicken RefSeq90 p, n 17465
        Neoaves          
           Columbiformes Columba-livia Rock pigeon RefSeq90 p, n 15562
           Ciconiiformes Pterocles-gutturalis Yellow-throated sandgrouse RefSeq90 p, n 14859
           Musophagiformes Tauraco-erythrolophus Red-crested turaco RefSeq90 p, n 14922
           Cuculiformes Cuculus-canorus Common cuckoo RefSeq90 p, n 14727
           Caprimulgiformes Antrostomus-carolinensis Chuck-will's-widow RefSeq90 p, n 15451
           Apodiformes Calypte-anna Anna's hummingbird RefSeq90 p, n 14543
  Chaetura-pelagica Chimney swift RefSeq90 p, n 14111
           Opisthocomiformes Opisthocomus-hoazin Hoatzin RefSeq90 p, n 13333
           Gruiformes Chlamydotis-macqueenii Macqueen's bustard RefSeq90 p, n 14661
  Mesitornis-unicolor Brown roatelo RefSeq90 p, n 15561
  Eurypyga-helias Sunbittern RefSeq90 p, n 14721
  Balearica-regulorum Grey crowned-crane RefSeq90 p, n 15006
           Charadriiformes Calidris-pugnax Ruff RefSeq90 p, n 16523
  Charadrius-vociferus Killdeer RefSeq90 p, n 14465
           Aequornithia          
              Gaviiformes Gavia-stellata Gharial RefSeq90 p, n 14665
              Sphenisciformes Pygoscelis-adeliae Adelie penguin RefSeq90 p, n 13734
  Aptenodytes-forsteri Emperor penguin RefSeq90 p, n 14550
              Procellariiformes Fulmarus-glacialis Northern fulmar RefSeq90 p, n 15108
              Pelecaniformes          
              Phaethontidae Phaethon-lepturus White-tailed tropicbird RefSeq90 p, n 15065
              Phalacrocoracidae Phalacrocorax-carbo Great cormorant RefSeq90 p, n 14394
              Ciconiiformes Pelecanus-crispus Dalmatian pelican RefSeq90 p, n 15254
  Nipponia-nippon Crested ibis RefSeq90 p, n 15018
  Egretta-garzetta Little egret RefSeq90 p, n 14127
           Strigiformes Athene-cunicularia Burrowing owl RefSeq90 p, n 13841
  Tyto-alba Barn owl RefSeq90 p, n 13915
           Coliiformes Colius-striatus Speckled mousebird RefSeq90 p, n 14900
           Trogoniformes Apaloderma-vittatum Bar-tailed trogon RefSeq90 p, n 14307
           Bucerotiformes Buceros-rhinoceros Rhinoceros hornbill RefSeq90 p, n 14401
           Coraciiformes Leptosomus-discolor Cuckoo roller RefSeq90 p, n 15196
  Merops-nubicus Carmine bee-eater RefSeq90 p, n 14559
           Piciformes Picoides-pubescens Downy woodpecker RefSeq90 p, n 14136
           Cariamiformes Cariama-cristata Red-legged seriema RefSeq90 p, n 14999
           Falconiformes Falco-cherrug Saker falcon RefSeq90 p, n 14695
  Falco-peregrinus Peregrine falcon RefSeq90 p, n 14847
  Aquila-chrysaetos Golden eagle RefSeq90 p, n 15637
  Haliaeetus-leucocephalus Bald eagle RefSeq90 p, n 15212
  Haliaeetus-albicilla White-tailed eagle RefSeq90 p, n 14895
           Psittaciformes Nestor-notabilis Kea RefSeq90 p, n 14740
  Melopsittacus-undulatus Budgerigar RefSeq90 p, n 14243
           Acanthisittidae Acanthisitta-chloris Rifleman RefSeq90 p, n 15052
           Corvidae Corvus-cornix Hooded crow RefSeq90 p, n 13622
  Corvus-brachyrhynchos American crow RefSeq90 p, n 14927
           Paridae Cyanistes-caeruleus Blue tit RefSeq90 p, n 16519
  Pseudopodoces-humilis Tibetan ground-tit RefSeq90 p, n 15801
  Parus-major Great tit RefSeq90 p, n 15240
           Muscicapidae Ficedula-albicollis Collared flycatcher Ens91 p, n 15303
  Ficedula-albicollis-1 Collared flycatcher RefSeq90 p, n 15387
           Sturnidae Sturnus-vulgaris Common starling RefSeq90 p, n 15233
           Passeroidea          
              Fringillidae Serinus-canaria Common canary RefSeq90 p, n 15584
              Pipridae Manacus-vitellinus Golden-collared manakin RefSeq90 p, n 16312
  Lepidothrix-coronata Blue-crowned manakin RefSeq90 p, n 15382
              Passerellidae Zonotrichia-albicollis White-throated sparrow RefSeq90 p, n 14377
              Thraupidae Geospiza-fortis Medium ground-finch RefSeq90 p, n 14183
              Estrildidae Taeniopygia-guttata Zebra finch Ens91 p, n 17488
  Taeniopygia-guttata-1 Zebra finch RefSeq90 p, n 16362
  Lonchura-striata White-rumped munia RefSeq90 p, n 15420
   Mammalia          
     Ornithorhynchus Ornithorhynchus-anatinus Platypus Ens92 p, n 21698
     Marsupialia Monodelphis-domestica Gray short-tailed opossum Ens92 p, n 21327
  Sarcophilus-harrisii Tasmanian devil Ens92 p, n 18788
  Notamacropus-eugenii Tammar wallaby Ens92 p, n 15290
  Vombatus-ursinus Common wombat Ens98 p, n 21203
  Phascolarctos-cinereus Koala Ens98 p, n 19833
     Xenarthra Dasypus-novemcinctus Nine-banded armadillo Ens92 p, n 22711
  Choloepus-hoffmanni Hoffmann's two-fingered sloth Ens92 p, n 12393
     Afrotheria          
         Afroinsectiphilia          
           Macroscelidea Elephantulus-edwardii Cape elephant shrew RefSeq p, n 20443
           Tubulidentata Orycteropus-afer Aardvark NCBI p, n 19498
           Chrysochloridae Chrysochloris-asiatica Cape golden mole RefSeq p, n 19625
           Tenrecidae Echinops-telfairi Madagascar hedgehog Ens92 p, n 16575
         Paenungulata          
           Hyracoidea Procavia-capensis Cape rock hyrax Ens92 p, n 16057
           Proboscidea Loxodonta-africana African elephant Ens92 p, n 20033
           Sirenia Trichechus-manatus Florida manatee NCBI p, n 19095
     Laurasiatheria          
       Eulipotyphla          
          Erinaceidae Erinaceus-europaeus Western European hedgehog Ens92 p, n 14601
          Soricidae Sorex-araneus European shrew Ens92 p, n 13187
          Talpidae Condylura-cristata Star-nosed mole RefSeq p, n 17882
       Chiroptera          
          Yinpterochiroptera          
             Rhinolophoidea Hipposideros-armiger Great roundleaf bat RefSeq p, n 18949
  Rhinolophus-sinicus Chinese rufous horseshoe bat RefSeq p, n 21417
             Pteropodidae Rousettus-aegyptiacus Egyptian fruit bat RefSeq p, n 19412
  Pteropus-alecto Black flying fox RefSeq p, n 18350
  Pteropus-vampyrus Large flying fox Ens92 p, n 16990
          Yangochiroptera          
             Phyllostomidae Desmodus-rotundus Common vampire bat RefSeq p, n 18618
  Phyllostomus-discolor Pale spear-nosed bat RefSeq p, n 19080
             Vespertilionidae Miniopterus-natalensis Natal long-fingered bat RefSeq p, n 18161
  Eptesicus-fuscus Big brown bat RefSeq p, n 18733
  Myotis-lucifugus Little brown bat Ens92 p, n 19728
       Perissodactyla          
          Rhinocerotidae Ceratotherium-simum White rhinoceros NCBI p, n 19971
          Equidae Equus-asinus-asinus Donkey Ens98 p, n 19963
  Equus-caballus Horse Ens92 p, n 20449
  Equus-przewalskii Przewalski's horse RefSeq p, n 21351
       Pholidota Manis-javanica Malayan pangolin NCBI p, n 21289
       Carnivora          
          Feliformia          
             Herpestidae Suricata-suricatta Meerkat RefSeq p, n 19608
             Felidae          
                Pantherinae Panthera-pardus Leopard Ens98 p, n 19690
  Panthera-pardus-1 Leopard RefSeq p, n 20305
  Panthera-tigris-altaica Tiger Ens98 p, n 17546
  Panthera-tigris-altaica-1 Tiger RefSeq p, n 18496
                Felinae Lynx-canadensis Lynx RefSeq p, n 19417
  Acinonyx-jubatus Cheetah RefSeq p, n 19655
  Puma-concolor Cougar RefSeq p, n 17646
  Felis-catus Domestic cat Ens98 p, n 19587
  Felis-catus-R Domestic cat RefSeq p, n 20374
          Caniformia          
             Canidae Vulpes-vulpes Red fox Ens98 p, n 20306
  Canis-lupus Grey wolf RefSeq p, n 20248
  Canis-familiaris Dog Ens92 p, n 19856
             Mustelidae Enhydra-lutris Sea otter RefSeq p, n 19327
  Neovison-vison American mink Ens98 p, n 19619
  Mustela-putorius-furo Ferret Ens92 p, n 19910
             Ursidae Ailuropoda-melanoleuca Giant panda Ens92 p, n 19343
  Ursus-americanus American black bear Ens98 p, n 20568
  Ursus-arctos Brown bear RefSeq p, n 19835
  Ursus-maritimus Polar bear NCBI p, n 19379
             Phocidae Neomonachus-schauinslandi-1 Hawaiian monk seal RefSeq p, n 18806
  Leptonychotes-weddellii Weddell seal RefSeq p, n 20535
             Odobenidae Odobenus-rosmarus-1 Walrus RefSeq p, n 19399
             Otariidae Zalophus-californianus California sea lion RefSeq p, n 19604
  Eumetopias-jubatus Steller sea lion RefSeq p, n 19655
  Callorhinus-ursinus Northern fur seal RefSeq p, n 21619
       Cetartiodactyla          
         Camelidae Vicugna-pacos Alpaca Ens92 p, n 11765
  Camelus-bactrianus Bactrian camel NCBI p, n 19158
  Camelus-dromedarius Dromedary camel RefSeq p, n 20049
         Suidae Sus-scrofa Pig Ens92 p, n 22452
  Sus-scrofa-1 Pig RefSeq89 p, n 20679
         Ruminantia          
            Cervidae Odocoileus-virginianus White-tailed deer NCBI p, n 21059
            Bovidae          
               Antilopinae Pantholops-hodgsonii Tibetan antelope RefSeq p, n 25481
  Ovis-aries Domestic sheep Ens92 p, n 20921
  Capra-hircus Domestic goat Ens92 p, n 21361
               Bovinae Bubalus-bubalis Water buffalo NCBI p, n 21532
  Bison-bison American bison NCBI p, n 20644
  Bos-mutus Wild yak Ens98 p, n 20850
  Bos-taurus Domestic cow Ens92 p, n 19994
  Bos-taurus-1 Domestic cow RefSeq89 p, n 21077
         Cetacea          
            Odontoceti Balaenoptera-acutorostrata Minke whale NCBI p, n 18400
            Mysticeti          
               Physeteridae Physeter-catodon Sperm whale NCBI p, n 19034
               Lipotidae Lipotes-vexillifer Yangtze River dolphin NCBI p, n 18877
               Phocoenidae Neophocaena-asiaeorientalis Narrow-ridged Finless Porpoise RefSeq p, n 18247
               Monodontidae Monodon-monoceros Narwhal RefSeq p, n 18377
  Delphinapterus-leucas Beluga whale RefSeq p, n 18456
               Delphinidae Lagenorhynchus-obliquidens Pacific white-sided dolphin RefSeq p, n 18409
  Orcinus-orca Killer whale NCBI p, n 18129
  Globicephala-melas Long-finned pilot whale RefSeq p, n 18542
  Tursiops-truncatus Bottlenose-dolphin Ens92 p, n 16550
     Euarchontoglires          
       Scandentia Tupaia-belangeri Common tree shrew Ens92 p, n 15471
  Tupaia-chinensis Chinese tree shrew RefSeq p, n 21077
       Glires          
         Lagomorpha Oryctolagus-cuniculus Domestic rabbit Ens92 p, n 19293
  Ochotona-princeps Southern American pika Ens92 p, n 16006
         Rodentia          
           Sciuridae Marmota-flaviventris Yellow-bellied marmot RefSeq p, n 20271
  Marmota-marmota Alpine marmot RefSeq p, n 20931
  Urocitellus-parryii Arctic ground squirrel RefSeq p, n 19359
  Ictidomys-tridecemlineatus Thirteen-lined ground squirrel Ens92 p, n 11525
           Hystricomorpha          
              Bathyergidae Fukomys-damarensis Damara mole rat Ens92 p, n 17730
  Heterocephalus-glaber Naked mole rat (female) Ens92 p, n 20774
              Octodontidae Octodon-degus Degu Ens92 p, n 19982
              Chinchillidae Chinchilla-lanigera Long-tailed chinchilla Ens92 p, n 17809
              Caviidae Cavia-porcellus Guinea pig Ens92 p, n 18095
  Cavia-aperea Brazilian guinea pig Ens92 p, n 14218
           Mouse-related          
              Heteromyidae Dipodomys-ordii Ord's kangaroo rat Ens92 p, n 16911
              Myomorpha          
                 Dipodidae Jaculus-jaculus Egyptian jerboa Ens92 p, n 17845
                 Muroidea          
                    Spalacidae Nannospalax-galili Upper Galilee mountains blind mole rat Ens92 p, n 18647
                    Cricetidae Peromyscus-maniculatus-bairdii North American deer mouse Ens92 p, n 19854
  Cricetulus-griseus Chinese hamster (CHOK1GS-HDv1) Ens92 p, n 20824
                    Muridae Rattus-norvegicus Norway rat Ens92 p, n 22250
  Rattus-norvegicus-1 Norway rat RefSeq89 p, n 23401
  Mus-pahari Gairdner's shrew-mouse Ens92 p, n 19611
  Mus-spretus Algerian mouse Ens92 p, n 20168
  Mus-musculus House mouse Ens91 p, n 22798
  Mus-musculus-1 House mouse RefSeq89 p, n 22070
     Dermoptera Galeopterus-variegatus Malayan flying lemur RefSeq p, n 22821
     Primates          
       Strepsirrhini Otolemur-garnettii Small-eared galago Ens92 p, n 19506
  Microcebus-murinus Gray mouse lemur NCBI p, n 20509
  Propithecus-coquereli Propithecus coquereli Ens92 p, n 17925
  Prolemur-simus Greater bamboo lemur Ens98 p, n 20354
       Haplorrhini          
         Tarsiiformes Carlito-syrichta Philippine tarsier Ens92 p, n 18398
         Simiiformes          
           Platyrrhini Aotus-nancymaae Ma's night monkey Ens92 p, n 20412
  Callithrix-jacchus Common marmoset Ens92 p, n 19690
  Cebus-capucinus White-faced capuchin Ens92 p, n 20317
  Saimiri-boliviensis-boliviensis Bolivian squirrel monkey Ens92 p, n 19380
           Catarrhini          
             Cercopithecidae          
               Colobinae Colobus-angolensis-palliatus Peters' Angolan colobus Ens91 p, n 20617
  Rhinopithecus-roxellana Golden snub-nosed monkey Ens91 p, n 21289
  Rhinopithecus-bieti Black snub-nosed monkey Ens91 p, n 20966
               Cercopithecinae Chlorocebus-sabaeus Green monkey Ens91 p, n 19165
  Papio-anubis Kenya baboon Ens91 p, n 21647
  Cercocebus-atys Sooty mangabey Ens91 p, n 20926
  Mandrillus-leucophaeus Drill Ens91 p, n 20841
  Macaca-nemestrina Pigtail macaqu Ens91 p, n 21060
  Macaca-fascicularis Crab eating macaque Ens91 p, n 21584
  Macaca-mulatta Rhesus macaque Ens91 p, n 21099
             Hominoidea          
               Hylobatidae Nomascus-leucogenys White-cheeked Gibbon Ens92 p, n 20794
               Hominidae Pongo-abelii Orangutan Ens92 p, n 20424
  Gorilla-gorilla Western gorilla Ens92 p, n 21794
  Pan-troglodytes Chimpanzee Ens92 p, n 23534
  Pan-paniscus Pygmy chimpanzee Ens92 p, n 21210
  Homo-sapiens-E102 Human Ens102 p, n 23483
  Homo-sapiens-E99 Human Ens99 p, n 23485
  Homo-sapiens Human Ens91 p, n 23070
  Homo-sapiens-1 Human RefSeq89 p, n 20101
Xenacoelomorpha          
 Xenoturbella Xenoturbella-bocki Xenoturbella TSA p, n 131373
 Nemertodermatida          
 Acoela Symsagittifera-roscoffensis Acoela TSA p, n 107641
  Hofstenia-miamia Acoela EnsMet48 p, n 22454
  Isodiametra-pulchra Acoela TSA p, n 181811
  Praesagittifera-naikaiensis Acoela OIST-S p, n 24410
           
Protostomia        
Spiralia          
  Rotifera Adineta-vaga Rotifer EnsMet39 p, n 49300
  Mesozoa   Intoshia-linei Orthonectid mesozoan Coming soon   Xxxx
    Dicyema-japonicum Dicyemid mesozoan Coming soon   Xxxx
  Platyhelminthes          
     Cestoda Echinococcus-granulosus Hydatid worm RefSeq90 p, n 11319
     Rhabditophora   Schmidtea-mediterranea Freshwater planarian flatworm Coming soon   Xxxx
     Trematoda Opisthorchis-viverrini Southeast Asian liver fluke RefSeq90 p, n 16356
  Schistosoma-haematobium Urinary blood fluke RefSeq90 p, n 10837
  Schistosoma-mansoni Blood fluke EnsMet40 p, n 10772
  Annelida Capitella-teleta Polychaete worm EnsMet39 p, n 32175
  Helobdella-robusta Californian leech EnsMet39 p, n 23432
  Nemertea Notospermus-geniculatus Ribbon worm OIST-S p, n 43294
  Phoronida Phoronis-australis Horseshoe worm OIST-S p, n 20473
  Brachiopoda Lingula-anatina Lamp shell EnsMet38 p, n 34105
  Cephalopoda Octopus-bimaculoides California two-spotted octopus EnsMet38 p, n 33609
  Octopus-bimaculoides-1 California two-spotted octopus RefSeq p, n 15842
  Octopus-vulgaris Common octopus RefSeq p, n 18183
  Gastropoda Pomacea-canaliculata Golden apple snail RefSeq p, n 21131
  Lottia-gigantea Giant owl limpet EnsMet38 p, n 23340
  Biomphalaria-glabrata Bloodfluke planorb NCBI p, n 25539
  Aplysia-californica California sea hare RefSeq p, n 19945
  Bivalvia Crassostrea-virginica Eastern oyster RefSeq p, n 34596
  Crassostrea-gigas Pacific oyster EnsMet40 p, n 26089
  Mizuhopecten-yessoensis Ezo giant scallop RefSeq p, n 24521
  Pinctada-fucata-1 Pearl oyster OIST-S v1 p, n 72595
  Pinctada-fucata Pearl oyster OIST-S v2 p, n 31477
Ecdysozoa          
  Priapulida Priapulus-caudatus Priapulid worm NCBI p, n 15088
  Halicryptus-spinulosus TSA p, n 4359
  Nematoda Trichinella-spiralis Trichina worm EnsMet39 p, n 16380
  Strongyloides-ratti Parasitic roundworm EnsMet39 p, n 12464
  Onchocerca-volvulus EnsMet39 p, n 12117
  Loa-loa Eye worm EnsMet39 p, n 14908
  Brugia-malayi Filarial nematode worm EnsMet39 p, n 11010
  Pristionchus-pacificus Parasitic nematode EnsMet39 p, n 29201
  Caenorhabditis-japonica Nematode worm EnsMet39 p, n 29931
  Caenorhabditis-brenneri Nematode worm EnsMet39 p, n 30674
  Caenorhabditis-remanei Nematode worm EnsMet39 p, n 31436
  Caenorhabditis-briggsae Nematode worm EnsMet39 p, n 22394
  Caenorhabditis-elegans Nematode worm EnsMet38 p, n 20222
  Caenorhabditis-elegans-1 Nematode worm RefSeq89 p, n 20090
  Chelicerata Limulus-polyphemus Atlantic horseshoe crab NCBI p, n 22860
  Sarcoptes-scabiei Itch mite EnsMet38 p, n 10471
  Tetranychus-urticae Red spider mite EnsMet38 p, n 17671
  Ixodes-scapularis Blacklegged tick EnsMet38 p, n 20486
  Centruroides-sculpturatus Bark scorpion NCBI p, n 24591
  Parasteatoda-tepidariorum House spider NCBI p, n 18601
  Stegodyphus-mimosarum African social velvet spider EnsMet38 p, n 27135
  Myriapoda Strigamia-maritima European centipede EnsMet38 p, n 14992
  Crustacea          
   Decapoda Penaeus-vannamei Pacific white shrimp RefSeq100 p, n 24974
  Penaeus-monodon Black tiger shrimp RefSeq210211 p, n 24079
  Hyalella-azteca Amphipod crustacean RefSeq p, n 18608
   Copepoda Eurytemora-affinis Copepod RefSeq p, n 20716
  Lepeophtheirus-salmonis Salmon louse EnsMet39 p, n 13081
   Branchiopoda Daphnia-magna Water flea EnsMet39 p, n 26646
  Daphnia-pulex Water flea EnsMet39 p, n 30590
  Hexapoda          
     Paraneoptera Pediculus-humanus Human lice EnsMet38 p, n 10786
     Dictyoptera Zootermopsis-nevadensis Dampwood termite EnsMet39 p, n 14610
  Cryptotermes-secundus Drywood termite NCBI p, n 12842
     Hemiptera Rhodnius-prolixus Triatomid bug EnsMet39 p, n 15064
  Acyrthosiphon-pisum Pea aphid EnsMet39 p, n 36195
     Hymenoptera Nasonia-vitripennis Parasitic wasp EnsMet39 p, n 17083
  Atta-cephalotes Leafcutter ant NCBI p, n 10491
  Solenopsis-invicta Imported red fire ant NCBI p, n 14453
  Apis-mellifera European honey bee EnsMet39 p, n 15314
  Bombus-impatiens Bumblebee EnsMet39 p, n 15896
  Bombus-terrestris Large earth bumblebee EnsMet39 p, n 10581
     Coleoptera Tribolium-castaneum Rust-red flour beetle EnsMet39 p, n 16590
  Anoplophora-glabripennis Asian long-horn beetle EnsMet39 p, n 22253
  Dendroctonus-ponderosae Mountain pine beetle EnsMet39 p, n 13088
     Lepidoptera Bombyx-mori Silkworm EnsMet38 p, n 14623
  Heliconius-melpomene Postman butterfly EnsMet39 p, n 12669
  Danaus-plexippus American monarch EnsMet39 p, n 15128
    Melitaea-cinxia Glanville fritillary EnsMet39 p, n 16629
     Diptera Belgica-antarctica Antarctic midge EnsMet39 p, n 13510
  Anopheles-darlingi African malaria mosquito EnsMet39 p, n 10509
  Culex-quinquefasciatus Southern house mosquito EnsMet39 p, n 18968
  Aedes-aegypti Yellow fever mosquito EnsMet39 p, n 15796
  Mayetiola-destructor Hessian fly EnsMet39 p, n 19927
  Megaselia-scalaris Humpbacked fly EnsMet39 p, n 11461
  Teleopsis-dalmanni Malaysian stalk-eyed fly EnsMet39 p, n 16570
  Lucilia-cuprina Australian sheep blowfly NCBI p, n 15536
  Drosophila-grimshawi Fruit fly EnsMet39 p, n 13705
  Drosophila-mojavensis Fruit fly EnsMet39 p, n 13425
  Drosophila-virilis Fruit fly EnsMet39 p, n 13620
  Drosophila-willistoni Fruit fly EnsMet39 p, n 13783
  Drosophila-pseudoobscura Fruit fly EnsMet39 p, n 14574
  Drosophila-persimilis Fruit fly EnsMet39 p, n 16874
  Drosophila-ananassae Fruit fly EnsMet39 p, n 14365
  Drosophila-yakuba Fruit fly EnsMet39 p, n 14824
  Drosophila-erecta Fruit fly EnsMet39 p, n 13605
  Drosophila-simulans Fruit fly EnsMet39 p, n 14179
  Drosophila-sechellia Fruit fly EnsMet39 p, n 16465
  Drosophila-melanogaster Fruit fly EnsMet38 p, n 13931
  Drosophila-melanogaster-1 Fruit fly RefSeq89 p, n 13918

  jinoue@g.ecc.u-tokyo.ac.jp