Supported host species¶
This page is generated from HostSpecies.csv, the curated host registry used by
MTD Explorer.
HostSpecies.csv tells MTD Explorer which host species can be resolved
automatically by Create_custom_host.sh, and which genome, annotation, and
protein reference metadata should be used.
Important
A species listed here is a curated host entry. For automatic custom-host creation, the entry also needs complete reference metadata, especially genome FASTA, GTF, protein FASTA, assembly, and reference status fields.
Summary¶
- Total curated host entries: 201
- Source file:
HostSpecies.csv
Reference-status counts:
COMPLETE: 200COMPLETE_OVERRIDE: 1
Main host list¶
Use this table to find the NCBI Taxon ID, scientific name, and common name of a host species.
| NCBI Taxon ID | Scientific name | Common name | Reference status | KEGG |
|---|---|---|---|---|
| 80966 | Acanthochromis polyacanthus | Spiny_chromis | COMPLETE | — |
| 9646 | Ailuropoda melanoleuca | Giant_panda | COMPLETE | aml |
| 61819 | Amphilophus citrinellus | Midas_cichlid | COMPLETE | — |
| 80972 | Amphiprion ocellaris | Clown_anemonefish | COMPLETE | aoce |
| 161767 | Amphiprion percula | Orange_clownfish | COMPLETE | — |
| 64144 | Anabas testudineus | Climbing_perch | COMPLETE | — |
| 8839 | Anas platyrhynchos | Mallard | COMPLETE | apla |
| 8840 | Anas platyrhynchos platyrhynchos | Common_mallard | COMPLETE | — |
| 28377 | Anolis carolinensis | Green_anole | COMPLETE | acs |
| 132585 | Anser brachyrhynchus | Pink_footed_goose | COMPLETE | abrc |
| 37293 | Aotus nancymaae | Ma_s_night_monkey | COMPLETE | anan |
| 223781 | Aquila chrysaetos chrysaetos | Golden_eagle | COMPLETE | achc |
| 8154 | Astatotilapia calliptera | Eastern_happy | COMPLETE | — |
| 7994 | Astyanax mexicanus | Mexican_tetra | COMPLETE | amex |
| 9771 | Balaenoptera musculus | Blue_whale | COMPLETE | bmus |
| 158456 | Betta splendens | Siamese_fighting_fish | COMPLETE | bspl |
| 6526 | Biomphalaria glabrata | Bloodfluke_planorb | COMPLETE | bgt |
| 43346 | Bison bison bison | American_bison | COMPLETE | bbis |
| 30521 | Bos grunniens | Domestic_yak | COMPLETE | — |
| 30522 | Bos indicus x Bos taurus | Hybrid_cattle | COMPLETE | — |
| 72004 | Bos mutus | Wild_yak | COMPLETE | bom |
| 9913 | Bos taurus | Cattle | COMPLETE | bta |
| 6239 | Caenorhabditis elegans | Nematode | COMPLETE | cel |
| 198806 | Calidris pugnax | Ruff | COMPLETE | narq |
| 9483 | Callithrix jacchus | White_tufted_ear_marmoset | COMPLETE | cjc |
| 7868 | Callorhinchus milii | Elephant_shark | COMPLETE | cmk |
| 9838 | Camelus dromedarius | Arabian_camel | COMPLETE | cdk |
| 286419 | Canis lupus dingo | Dingo | COMPLETE | clud |
| 9615 | Canis lupus familiaris | Dog | COMPLETE | cfa |
| 9925 | Capra hircus | Goat | COMPLETE | chx |
| 7957 | Carassius auratus | Goldfish | COMPLETE | caua |
| 1868482 | Carlito syrichta | Philippine_tarsier | COMPLETE | csyr |
| 51154 | Catagonus wagneri | Chacoan_peccary | COMPLETE | — |
| 10141 | Cavia porcellus | Domestic_guinea_pig | COMPLETE | cpoc |
| 2715852 | Cebus capucinus imitator | Panamanian_white_faced_capuchin | COMPLETE | cimi |
| 9531 | Cercocebus atys | Sooty_mangabey | COMPLETE | caty |
| 84702 | Cervus hanglu yarkandensis | Yarkand_deer | COMPLETE | — |
| 106734 | Chelonoidis abingdonii | Abingdon_island_giant_tortoise | COMPLETE | cabi |
| 34839 | Chinchilla lanigera | Long_tailed_chinchilla | COMPLETE | — |
| 60711 | Chlorocebus sabaeus | African_green_monkey | COMPLETE | csab |
| 9358 | Choloepus hoffmanni | Hoffmann_s_two_fingered_sloth | COMPLETE | — |
| 8478 | Chrysemys picta bellii | Western_painted_turtle | COMPLETE | cpic |
| 7719 | Ciona intestinalis | Sea_squirt_Ciona_intestinalis | COMPLETE | cin |
| 51511 | Ciona savignyi | Sea_squirt_Ciona_savignyi | COMPLETE | — |
| 7950 | Clupea harengus | Atlantic_herring | COMPLETE | char |
| 56716 | Cottoperca gobio | Channel_bull_blenny | COMPLETE | cgob |
| 93934 | Coturnix japonica | Japanese_quail | COMPLETE | cjo |
| 8502 | Crocodylus porosus | Australian_saltwater_crocodile | COMPLETE | cpoo |
| 8103 | Cyclopterus lumpus | Lumpfish | COMPLETE | clum |
| 244447 | Cynoglossus semilaevis | Tongue_sole | COMPLETE | csem |
| 28743 | Cyprinodon variegatus | Sheepshead_minnow | COMPLETE | cvg |
| 7962 | Cyprinus carpio | Common_carp | COMPLETE | ccar |
| 7955 | Danio rerio | Zebrafish | COMPLETE | dre |
| 9361 | Dasypus novemcinctus | Nine_banded_armadillo | COMPLETE | dnm |
| 9749 | Delphinapterus leucas | Beluga_whale | COMPLETE | dle |
| 299321 | Denticeps clupeoides | Denticle_herring | COMPLETE | — |
| 13489 | Dicentrarchus labrax | European_seabass | COMPLETE | — |
| 10020 | Dipodomys ordii | Ord_s_kangaroo_rat | COMPLETE | dord |
| 7227 | Drosophila melanogaster | Fruit_fly | COMPLETE | dme |
| 9371 | Echinops telfairi | Small_Madagascar_hedgehog | COMPLETE | etf |
| 8005 | Electrophorus electricus | Electric_eel | COMPLETE | eee |
| 7764 | Eptatretus burgeri | Inshore_hagfish | COMPLETE | — |
| 83772 | Equus asinus asinus | Donkey | COMPLETE_OVERRIDE | — |
| 9796 | Equus caballus | Horse | COMPLETE | ecb |
| 9365 | Erinaceus europaeus | Western_European_hedgehog | COMPLETE | — |
| 27687 | Erpetoichthys calabaricus | Reedfish | COMPLETE | — |
| 8010 | Esox lucius | Northern_pike | COMPLETE | els |
| 9685 | Felis catus | Domestic_cat | COMPLETE | fca |
| 59894 | Ficedula albicollis | Collared_flycatcher | COMPLETE | fab |
| 8078 | Fundulus heteroclitus | Mummichog | COMPLETE | — |
| 8049 | Gadus morhua | Atlantic_cod | COMPLETE | gmh |
| 9031 | Gallus gallus | Chicken | COMPLETE | gga |
| 69293 | Gasterosteus aculeatus | Three_spined_stickleback | COMPLETE | gat |
| 48883 | Geospiza fortis | Medium_ground_finch | COMPLETE | gfr |
| 1825980 | Gopherus evgoodei | Goodes_thornscrub_tortoise | COMPLETE | — |
| 9595 | Gorilla gorilla gorilla | Western_Lowland_Gorilla | COMPLETE | ggo |
| 8153 | Haplochromis burtoni | Burton_s_mouthbrooder | COMPLETE | — |
| 10181 | Heterocephalus glaber | Naked_mole_rat | COMPLETE | hgl |
| 109280 | Hippocampus comes | Tiger_tail_seahorse | COMPLETE | hcq |
| 9606 | Homo sapiens | Human | COMPLETE | hsa |
| 62062 | Hucho hucho | Huchen | COMPLETE | — |
| 7998 | Ictalurus punctatus | Channel_catfish | COMPLETE | ipu |
| 43179 | Ictidomys tridecemlineatus | Thirteen_lined_ground_squirrel | COMPLETE | iti |
| 51337 | Jaculus jaculus | Lesser_Egyptian_jerboa | COMPLETE | — |
| 37003 | Kryptolebias marmoratus | Mangrove_rivulus | COMPLETE | kmr |
| 56723 | Labrus bergylta | Ballan_wrasse | COMPLETE | — |
| 215358 | Larimichthys crocea | Large_yellow_croaker | COMPLETE | lco |
| 8187 | Lates calcarifer | Barramundi_perch | COMPLETE | lcf |
| 8630 | Laticauda laticaudata | Blue_ringed_sea_krait | COMPLETE | — |
| 7897 | Latimeria chalumnae | Coelacanth | COMPLETE | lcm |
| 7918 | Lepisosteus oculatus | Spotted_gar | COMPLETE | loc |
| 445787 | Leptobrachium leishanense | Leishan_spiny_toad | COMPLETE | — |
| 9785 | Loxodonta africana | African_savanna_elephant | COMPLETE | lav |
| 9541 | Macaca fascicularis | Crab_eating_macaque | COMPLETE | mcf |
| 9544 | Macaca mulatta | Macaque | COMPLETE | mcc |
| 9545 | Macaca nemestrina | Pig_tailed_macaque | COMPLETE | mni |
| 9568 | Mandrillus leucophaeus | Drill | COMPLETE | mleu |
| 9994 | Marmota marmota marmota | Alpine_marmot | COMPLETE | mmma |
| 205130 | Mastacembelus armatus | Zig_zag_eel | COMPLETE | — |
| 106582 | Maylandia zebra | Zebra_mbuna | COMPLETE | mze |
| 9103 | Meleagris gallopavo | Turkey | COMPLETE | mgp |
| 10036 | Mesocricetus auratus | Golden_Hamster | COMPLETE | maua |
| 30608 | Microcebus murinus | Gray_mouse_lemur | COMPLETE | mmur |
| 79684 | Microtus ochrogaster | Vole | COMPLETE | — |
| 13616 | Monodelphis domestica | Gray_short_tailed_opossum | COMPLETE | mdo |
| 40151 | Monodon monoceros | Narwhal | COMPLETE | — |
| 68415 | Moschus moschiferus | Siberian_musk_deer | COMPLETE | — |
| 10089 | Mus caroli | Ryukyu_mouse | COMPLETE | mcal |
| 10090 | Mus musculus | Mouse | COMPLETE | mmu |
| 10093 | Mus pahari | Shrew_mouse | COMPLETE | mpah |
| 10103 | Mus spicilegus | Steppe_mouse | COMPLETE | — |
| 10096 | Mus spretus | Western_wild_mouse | COMPLETE | — |
| 9669 | Mustela putorius furo | Domestic_ferret | COMPLETE | mpuf |
| 59463 | Myotis lucifugus | Little_brown_bat | COMPLETE | mlf |
| 586833 | Myripristis murdjan | Pinecone_soldierfish | COMPLETE | — |
| 35670 | Naja naja | Indian_cobra | COMPLETE | — |
| 1026970 | Nannospalax galili | Upper_Galilee_mountains_blind_mole_rat | COMPLETE | ngi |
| 32507 | Neolamprologus brichardi | Lyretail_cichlid | COMPLETE | — |
| 452646 | Neovison vison | American_mink | COMPLETE | nvs |
| 61853 | Nomascus leucogenys | Northern_white_cheeked_gibbon | COMPLETE | nle |
| 9315 | Notamacropus eugenii | Tammar_wallaby | COMPLETE | — |
| 8663 | Notechis scutatus | Mainland_tiger_snake | COMPLETE | nss |
| 105023 | Nothobranchius furzeri | Turquoise_killifish | COMPLETE | nfu |
| 9978 | Ochotona princeps | American_pika | COMPLETE | opi |
| 10160 | Octodon degus | Degu | COMPLETE | — |
| 8019 | Oncorhynchus kisutch | Coho_salmon | COMPLETE | oki |
| 8022 | Oncorhynchus mykiss | Rainbow_trout | COMPLETE | omy |
| 74940 | Oncorhynchus tshawytscha | Chinook_salmon | COMPLETE | otw |
| 8128 | Oreochromis niloticus | Nile_tilapia | COMPLETE | onl |
| 9258 | Ornithorhynchus anatinus | Platypus | COMPLETE | oaa |
| 9986 | Oryctolagus cuniculus | Rabbit | COMPLETE | ocu |
| 123683 | Oryzias javanicus | Javanese_ricefish | COMPLETE | — |
| 8090 | Oryzias latipes | Japanese_medaka_HdrR | COMPLETE | ola |
| 30732 | Oryzias melastigma | Indian_medaka | COMPLETE | oml |
| 183150 | Oryzias sinensis | Chinese_medaka | COMPLETE | — |
| 30611 | Otolemur garnettii | Small_eared_galago | COMPLETE | oga |
| 9940 | Ovis aries | Sheep | COMPLETE | oas |
| 9597 | Pan paniscus | Bonobo | COMPLETE | pps |
| 9598 | Pan troglodytes | Chimpanzee | COMPLETE | ptr |
| 9689 | Panthera leo | Lion | COMPLETE | plez |
| 9691 | Panthera pardus | Leopard | COMPLETE | ppad |
| 74533 | Panthera tigris altaica | Tiger | COMPLETE | ptg |
| 9555 | Papio anubis | Olive_baboon | COMPLETE | panu |
| 1676925 | Paramormyrops kingsleyae | Paramormyrops_kingsleyae | COMPLETE | pki |
| 9157 | Parus major | Great_Tit | COMPLETE | pmaj |
| 13735 | Pelodiscus sinensis | Chinese_softshell_turtle | COMPLETE | pss |
| 230844 | Peromyscus maniculatus bairdii | Northern_American_deer_mouse | COMPLETE | pmav |
| 7757 | Petromyzon marinus | Sea_lamprey | COMPLETE | pmrn |
| 38626 | Phascolarctos cinereus | Koala | COMPLETE | pcw |
| 42100 | Phocoena sinus | Vaquita | COMPLETE | psiu |
| 9755 | Physeter catodon | Sperm_whale | COMPLETE | pcad |
| 64176 | Podarcis muralis | Common_wall_lizard | COMPLETE | pmua |
| 48698 | Poecilia formosa | Amazon_molly | COMPLETE | pfor |
| 48699 | Poecilia latipinna | Sailfin_molly | COMPLETE | plai |
| 8081 | Poecilia reticulata | Guppy | COMPLETE | pret |
| 9601 | Pongo abelii | Sumatran_orangutan | COMPLETE | pon |
| 9813 | Procavia capensis | Cape_rock_hyrax | COMPLETE | — |
| 1328070 | Prolemur simus | Greater_bamboo_lemur | COMPLETE | — |
| 379532 | Propithecus coquereli | Coquerel_s_sifaka | COMPLETE | pcoq |
| 8673 | Pseudonaja textilis | Eastern_brown_snake | COMPLETE | ptex |
| 132908 | Pteropus vampyrus | Large_flying_fox | COMPLETE | pva |
| 303518 | Pundamilia nyererei | Makobe_Island_cichlid | COMPLETE | — |
| 42514 | Pygocentrus nattereri | Red_bellied_piranha | COMPLETE | — |
| 10116 | Rattus norvegicus | Norway_rat | COMPLETE | rno |
| 59479 | Rhinolophus ferrumequinum | Greater_horseshoe_bat | COMPLETE | rfq |
| 61621 | Rhinopithecus bieti | Black_snub_nosed_monkey | COMPLETE | rbb |
| 61622 | Rhinopithecus roxellana | Golden_snub_nosed_monkey | COMPLETE | rro |
| 559292 | Saccharomyces cerevisiae | Baker_s_yeast | COMPLETE | sce |
| 39432 | Saimiri boliviensis boliviensis | Bolivian_squirrel_monkey | COMPLETE | sbq |
| 8030 | Salmo salar | Atlantic_salmon | COMPLETE | sasa |
| 8032 | Salmo trutta | Brown_trout | COMPLETE | stru |
| 96440 | Salvator merianae | Argentine_black_and_white_tegu | COMPLETE | — |
| 283035 | Sander lucioperca | Pike_perch | COMPLETE | sluc |
| 9305 | Sarcophilus harrisii | Tasmanian_devil | COMPLETE | shr |
| 55149 | Sciurus vulgaris | Eurasian_red_squirrel | COMPLETE | svul |
| 113540 | Scleropages formosus | Asian_bonytongue | COMPLETE | sfm |
| 52904 | Scophthalmus maximus | Turbot | COMPLETE | smau |
| 9135 | Serinus canaria | Common_canary | COMPLETE | scan |
| 41447 | Seriola dumerili | Greater_amberjack | COMPLETE | sdu |
| 1841481 | Seriola lalandi dorsalis | Yellowtail_amberjack | COMPLETE | slal |
| 75366 | Sinocyclocheilus grahami | Golden_line_barbel | COMPLETE | sgh |
| 42254 | Sorex araneus | European_shrew | COMPLETE | sara |
| 8175 | Sparus aurata | Gilthead_seabream | COMPLETE | — |
| 8508 | Sphenodon punctatus | Tuatara | COMPLETE | — |
| 144197 | Stegastes partitus | Bicolor_damselfish | COMPLETE | — |
| 2489341 | Strigops habroptila | Kakapo | COMPLETE | shab |
| 441894 | Struthio camelus australis | African_ostrich | COMPLETE | scam |
| 9823 | Sus scrofa | Pig | COMPLETE | ssc |
| 59729 | Taeniopygia guttata | Zebra_finch | COMPLETE | tgu |
| 2587831 | Terrapene carolina triunguis | Three_toed_box_turtle | COMPLETE | — |
| 99883 | Tetraodon nigroviridis | Spotted_green_pufferfish | COMPLETE | tng |
| 37347 | Tupaia belangeri | Northern_tree_shrew | COMPLETE | tup |
| 9739 | Tursiops truncatus | Bottlenosed_dolphin | COMPLETE | — |
| 9999 | Urocitellus parryii | Arctic_ground_squirrel | COMPLETE | — |
| 9643 | Ursus americanus | American_black_bear | COMPLETE | uar |
| 29073 | Ursus maritimus | Polar_bear | COMPLETE | umr |
| 30538 | Vicugna pacos | Alpaca | COMPLETE | vpc |
| 29139 | Vombatus ursinus | Common_wombat | COMPLETE | — |
| 9627 | Vulpes vulpes | Red_fox | COMPLETE | vvp |
| 8364 | Xenopus tropicalis | Tropical_clawed_frog | COMPLETE | xtr |
| 8083 | Xiphophorus maculatus | Southern_platyfish | COMPLETE | xma |
How to use a listed host¶
If the host appears in this table and has complete reference metadata, create the host reference with automatic mode:
Then run MTD Explorer using the same Taxon ID:
bash ~/MTD/MTD_explorer.sh \
-i /path/to/samplesheet.csv \
-o /path/to/output_directory \
-h <host_taxon_id>
If a species is not listed¶
If the host species is not present in HostSpecies.csv, use manual mode and
provide the genome FASTA, GTF annotation, and protein FASTA directly:
bash Create_custom_host.sh \
--ncbi-taxon-id <host_taxon_id> \
--scientific-name "Genus species" \
--genome /path/to/genome.fa.gz \
--gtf-file /path/to/annotation.gtf.gz \
--protein-fasta /path/to/proteins.fa.gz
See Custom host references for details.
KEGG column¶
The KEGG column is useful for checking whether species-specific KEGG mapping may be available.
A missing KEGG value does not necessarily mean the host cannot be used. It means KEGG-specific outputs may be limited. MTD Explorer can still use protein FASTA and GTF information to build eggNOG and GO-derived resources, including a master GMT for ssGSEA.
Notes¶
- Prefer one genome source and one release for genome FASTA, GTF, and protein FASTA.
- For automatic mode, use the Taxon ID listed in the table.
- For manual mode, use the Taxon ID of the species being analyzed and provide matching reference files.
- If a species uses a reference from another related species, check the
reference metadata in
HostSpecies.csvbefore interpreting host results.