ORTHOSCOPE v1.5.8: Vertebrates
Gene tree and orthogroup estimation using a species tree (< 5 min as default). 19 Oct. 2025
Instructions, Species tree Support: Safari, Firefox, Chrome yurai
Focal group    
Actinopterygians Mammals Vertebrates Deuterostomes Protostomes Acropora Plants
Status
Ready.
 
Mode Estimate gene tree Compare gene and species trees Download gene models
Query sequences (fasta format): DNA  Amino acid  Example fasta file: DNA, Amino acid
 
  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%
Key node Olfactore, Chordata, Deuterostomia, or Bilateria
Node name in rearranged gene tree BSvalue   BSvalue_Classification_DupState  
Gene description in gene tree leaf Shown   Not shown  
             
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          
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
  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
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
           
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
  Ciona-intestinalis-KY21 Transparent sea squirt Ghost KY21 p, n 18788
 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            
    Holocephali Callorhinchus-milii Elephant shark RefSeq89 p, n 17847
  Callorhinchus-milii-E102 Elephant shark Ens102 p, n 19415
    Elasmobranchii            
       Batoidea
          Torpediniformes
          Rajiformes
             Rajiidae Leucoraja-erinacea Little skate RefSeq240129 p, n 18957
  Amblyraja-radiata-N Thorny skate RefSeq200601 p, n 18475
          Rhinopristiformes Pristis-pectinata Smalltooth sawfish RefSeq221218 p, n 17434
          Myliobatiformes
             Dasyatidae Hemitrygon-akajei xxxx
  Hypanus-sabinus Atlantic stingray RefSeq240129 p, n 22522
       Selachii          
          Squalomorphii          
          Galeomorphii          
             Orectolobiformes          
                Hemiscylliidae Chiloscyllium-punctatum Brownbanded bamboo shark Squalomix p, n 34038
  Chiloscyllium-plagiosum Whitespotted bambooshark RefSeq220701 p, n 19903
                Stegostomatidae Stegostoma-fasciatum Torafuzame RefSeq220701 p, n 18281
  Stegostoma-tigrinum Zebra shark RefSeq240129 p, n 19223
                Rhincodontidae Rhincodon-typus Whale shark RefSeq89 p, n 21868
  Rhincodon-typus-R Whale shark Squalomix p, n 27005
             Lamniformes Carcharodon-carcharias Great white shark RefSeq p, n 19427
             Carcharhiniformes Scyliorhinus-torazame Cloudy catshark Squalomix p, n 28051
  Scyliorhinus-canicula Smaller spotted catshark RefSeq210206 p, n 20561
 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 Lyretail 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          
            Mysticeti Balaenoptera-acutorostrata Minke whale NCBI p, n 18400
            Odontoceti          
               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
  jinoueATg.ecc.u-tokyo.ac.jp