Species included 



A. Species ID

The table below lists all species based on genome-wide sequence resources (not based on  NCBI Protein or GenBank) covered at aLeaves. Please see the 'Database' page for the sources of the sequences of individual species. Species newly added in the latest aLeaves update are indicated with '*'If you proceed to the MAFFT server for data set refinement and tree inference, these Species IDs will be automatically recognized, and the sequences will be colored accordingly.

Species ID Latin species name English common name Category
HOMSA Homo sapiens human Mammals
AILME Ailuropoda melanoleuca giant panda Mammals
BOSTA Bos taurus cow Mammals
CALJA Callithrix jacchus marmoset Mammals
CANFA Canis familiaris dog Mammals
CAVPO Cavia porcellus Guinea pig Mammals
CHOHO Choloepus hoffmanni two-toed sloth Mammals
DASNO Dasypus novemcinctus nine-banded armadillo Mammals
DIPOR Dipodomys ordii kangaroo rat Mammals
ECHTE Echinops telfairi small Madagascan hedgehog tenrec Mammals
EQUCA Equus caballus horse Mammals
ERIEU Erinaceus europaeus western European hedgehog Mammals
FELCA Felis catus cat Mammals
GORGO Gorilla gorilla Western lowland gorilla Mammals
ICTTR Ictidomys tridecemlineatus thirteen-lined ground squirrel Mammals
LOXAF Loxodonta africana African elephant Mammals
MACMU Macaca mulatta rhesus monkey Mammals
MICMU Microcebus murinus mouse lemur Mammals
MUSMU Mus musculus mouse Mammals
MUSPU Mustela putorius furo ferret Mammals
MYOLU Myotis lucifugus little brown bat Mammals
NOMLE Nomascus leucogenys Northern white-cheeked gibbon Mammals
OCHPR Ochotona princeps American pika Mammals
ORYCU Oryctolagus cuniculus rabbit Mammals
OTOGA Otolemur garnettii bushbaby Mammals
PANTR Pan troglodytes chimpanzee Mammals
PAPAN Papio anubis olive baboon Mammals
PONAB Pongo abelii orangutan Mammals
PROCA Procavia capensis rock hyrax Mammals
PTEVA Pteropus vampyrus megabat Mammals
RATNO Rattus norvegicus rat Mammals
SORAR Sorex araneus shrew Mammals
SUSSC Sus scrofa pig Mammals
OVIAR Ovis aries sheep Mammals
TARSY Tarsius syrichta Tasmanian devil Mammals
TUPBE Tupaia belangeri tree shrew Mammals
TURTR Tursiops truncatus dolphin Mammals
VICPA Vicugna pacos alpaca Mammals
MACEU Macropus eugenii  tammar wallaby Mammals
SARHA Sarcophilus harrisii Tasmanian devil Mammals
MONDO Monodelphis domestica  opossum Mammals
ORNAN Ornithorhynchus anatinus platypus Mammals
GALGA Gallus gallus chicken Sauropsids (reptiles/birds)
MELGA Meleagris gallopavo turkey Sauropsids (reptiles/birds)
TAEGU Taeniopygia guttata  Zebra Finch Sauropsids (reptiles/birds)
ANOCA Anolis carolinensis Anole lizard Sauropsids (reptiles/birds)
PELSI Pelodiscus sinensis soft-shelled turtle Sauropsids (reptiles/birds)
CHEMY Chelonia mydas green sea turtle Sauropsids (reptiles/birds)
CHRPI Chrysemys picta painted turtle Sauropsids (reptiles/birds)
ALLSI Alligator sinensis Chinese alligator Sauropsids (reptiles/birds)
XENTR Xenopus tropicalis Western clawed frog Non-amniote sarcopterygian
LATCH Latimeria chalumnae Coelacanth Non-amniote sarcopterygian
ORYLA Oryzias latipes medaka Actinopterygian fish
TAKRU Takifugu rubripes  Fugu Actinopterygian fish
TETNI Tetraodon nigroviridis  Tetraodon Actinopterygian fish
DANRE Danio rerio  Zebrafish Actinopterygian fish
GADMO Gadus morhua Atlantic cod Actinopterygian fish
ORENI Oreochromis niloticus Nile tilapia Actinopterygian fish
GASAC Gasterosteus aculeatus stickleback Actinopterygian fish
XIPMA Xiphophorus maculatus platyfish Actinopterygian fish
ASTME Astyanax mexicanum Mexican cavefish Actinopterygian fish
POEFO Poecilia formosa Amazon molly Actinopterygian fish
LEPOC Lepisosteus oculatus spotted gar Actinopterygian fish
CALMI Callorhinchus milii ghost shark Cartilaginous fishes (Chondrichthyes)
PETMA Petromyzon marinus  sea lamprey Cyclostomes
LETJA Lethenteron japonicum (Lethenteron camtschaticum)  Japanese lamprey Cyclostomes
CIOSA Ciona savignyi (sea squirt) Invertebrate deuterostome
CIOIN Ciona intestinalis (vase tunicate) Invertebrate deuterostome
OIKDI Oikopleura dioica  Invertebrate deuterostome
BRAFL Branchiostoma floridae (lancelet) Invertebrate deuterostome
STRPU Strongylocentrotus purpuratus purple sea urchin Invertebrate deuterostome
DAPPU Daphnia pulex waterflea  Arthropod
PEDHU Pediculus humanus human louse  Arthropod
ATTCE Atta cephalotes leaf cutter ant  Arthropod
SOLIN Solenopsis invicta red fire ant  Arthropod
APIME Apis mellifera honeybee Arthropod
DANPL Danaus plexippus monarch butterfly Arthropod
BOMMO Bombyx mori silkworm  Arthropod
ANOGA Anopheles gambiae African malaria mosquito  Arthropod
ACYPI Acyrthosiphon pisum pea aphid Arthropod
AEDAE Aedes aegypti yellow fever mosquito Arthropod
CULQU Culex quinquefasciatus house mosquito Arthropod
DROME Drosophila melanogaster (fruitfly) Arthropod
DROAN Drosophila ananassae (fruitfly) Arthropod
DROER Drosophila erecta (fruitfly) Arthropod
DROGR Drosophila grimshawi (fruitfly) Arthropod
DROMO Drosophila mojavensis (fruitfly) Arthropod
DROPE Drosophila persimilis (fruitfly) Arthropod
DROPS Drosophila pseudoobscura (fruitfly) Arthropod
DROSE Drosophila sechellia (fruitfly) Arthropod
DROSI Drosophila simulans (fruitfly) Arthropod
DROVI Drosophila virilis (fruitfly) Arthropod
DROWI Drosophila willistoni (fruitfly) Arthropod
DROYA Drosophila yakuba (fruitfly) Arthropod
HELME Heliconius melpomene postman butterfly Arthropod
TRICA Tribolium castaneum red flour beetle Arthropod
DENPO Dendroctonus ponderosae mountain pine beetle Arthropod
NASVI Nasonia vitripennis wasp Arthropod
STRMA Strigamia maritima
Arthropod
IXOSC Ixodes scapularis black-legged tick Arthropod
TETUR Tetranychus urticae  two-spotted spider mite Arthropod
MEGSC Megaselia scalaris coffin fly Arthropod
RHOPR Rhodnius prolixus Arthropod
MELCI Melitaea cinxia Glanville fritillary Arthropod
ZOONE Zootermopsis nevadensis termite Arthropod
BELAN Belgica antarctica* Antarctic midge Arthropod
BOMIM Bombus impatiens* common eastern bumblebee Arthropod
LEPSA Lepeophtheirus salmonis* sea louse Arthropod
LUCCU Lucilia cuprina* Australian sheep blowfly Arthropod
SARSC Sarcoptes scabiei* itch mite Arthropod
STEMI Stegodyphus mimosarum* African social velvet spider Arthropod
PRIPA Pristionchus pacificus Nematode
LOALO Loa loa eye worm Nematode
TRISP Trichinella spiralis Nematode
CAEEL Caenorhabditis elegans Nematode
CAEBR Caenorhabditis brigssae Nematode
CAEJA Caenorhabditis japonica Nematode
CAEBE Caenorhabditis brenneri Nematode
CAERE Caenorhabditis remanei  Nematode
MELIN Meloidogyne incognita Nematode
BRUMA Brugia malayi filarial nematode parasite Nematode
ONCVO Onchocerca volvolus Nematode
STRRA Strongyloides ratti* rat threadworm Nematode
SCHJA Schistosoma japonicum blood fluke Lophotrochozoan
SCHMA Schistosoma mansoni blood fluke Lophotrochozoan
CAPTE Capitella teleta polycheate worm Lophotrochozoan
HELRO Helobdella robusta leech Lophotrochozoan
PINFU Pinctada fucata pearl oyster Lophotrochozoan
CRAGI Crassostrea gigas Pacific oyster Lophotrochozoan
OCTBI Octopus bimaculoides* California two-spot octopus Lophotrochozoan
LINAN Lingula anatina* brachiopod Lophotrochozoan
THEKI Thelohanellus kitauei* myxosporean Non-bilaterian
TRIAD Trichoplax adherens Non-bilaterian
NEMVE Nematostella vectensis sea anemone Non-bilaterian
ACRDI Acropora digitifera coral Non-bilaterian
HYDMA Hydra magnipapillata hydra Non-bilaterian
MNELE Mnemiopsis leidyi comb jellyfish Non-bilaterian
AMPQU Amphimedon queenslandica sponge Non-bilaterian

Unofficial English names just for users' information are found in parentheses.


B. Category ID

Most of the sequences retrieved from NCBI Protein (or GenBank) originally have full species names instead of Species ID listed above. Plus, we have added Category ID at the beginning of sequence title lines. If you proceed to the MAFFT server for data set refinement and tree inference, these Category IDs will also be automatically recognized, and the sequences will be colored accordingly.


Category ID Correspondence to aLeaves Databases Group
MAM Database 1-4 Mammals
SAU Database 5 Sauropsids (reptiles/birds)
SAR Database 5 Non-amniote sarcopterygians
ACT Database 5 Actinopterygians
NOS Database 6 Non-osteichthyan vertebrates (Cartilaginous fishes and cyclostomes)
DEU Database 8 Invertebrate deuterostomes
ART Database 9 Arthropods
NEM Database 10 Nematodes
BIL Database 11 Bilaterians (excluding Arthropods, Nematodes and deuterostomes)
NBI Database 12 Non-bilaterian metazoans

For your detailed information, Database 7 is composed of annotated sequences in the categories SAU, SAR, ACT and NOS. Likewise, Database 13 is composed of annotated sequences in the categories DEU, ART, NEM, BIL and NBI.


Notes
Please contact the chief administrator of aLeaves, Shigehiro Kuraku, if you know of any source of sequences that seems more authentic or comprehensive than the one covered here.


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