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, common name,
reference status, and curated KEGG organism code of a host species. A dash (—)
in the KEGG column means that no compatible current KEGG organism code is
assigned to that curated host entry.
| 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 | — |
| 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 | eai |
| 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 | pvp |
| 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. KEGG organism codes in HostSpecies.csv are validated
against current KEGG genome-to-NCBI-Taxonomy mappings by
aux_scripts/orgdb/audit_hostspecies_kegg.py.
A missing KEGG value (— in the table) does not mean that the host cannot be
used. It means that no compatible current KEGG organism code was identified for
that curated host entry, so species-specific KEGG 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.
KEGG codes are not inferred from species names or abbreviations. Existing codes are checked against the NCBI Taxon ID, curated reference Taxon ID, and species-level taxonomy before they are accepted.
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.