SUPERFAMILY dataset

Genomes in each dataset are identified with a unique 10-character code:
e.g. EMeCh_Hsap
E the initial letter represents the superkingdom (Eukaryota)
MeCh the following four characters indicate intermediate taxonomic levels (in this case Metazoa and Chordata)
Hsap the final quartet is chosen for uniqueness from the genus,species, and, in certain cases, strain names.


Genomes removed from the datasets in constructing phylogenetic trees are marked 1
Genome code Species Genome code Species
ACrTh_Aper Aeropyrum_pernix_K1 BFuFu_Fnuc Fusobacterium_nucleatum_ssp._nucleatum_ATCC_25586
ACrTh_Paer Pyrobaculum_aerophilum_IM2 BPlPl_Psp. 1 Pirellula_sp._1
ACrTh_Ssol Sulfolobus_solfataricus_P2 BPrAl_Atum 1 Agrobacterium_tumefaciens_C58
ACrTh_Stok Sulfolobus_tokodaii_7 BPrAl_Bhen 1 Bartonella_henselae_Houston-1
AEuAr_Aful Archaeoglobus_fulgidus_DSM_4304 BPrAl_Bjap Bradyrhizobium_japonicum_USDA_110
AEuHa_Hsp. Halobacterium_sp._NRC-1 BPrAl_Bmel Brucella_melitensis_16M
AEuMe_Mace Methanosarcina_acetivorans_C2A BPrAl_Bqui 1 Bartonella_quintana_Toulouse
AEuMe_Mjan Methanocaldococcus_jannaschii_DSM_2661 BPrAl_Bsui Brucella_suis_1330
AEuMe_Mkan Methanopyrus_kandleri_AV19 BPrAl_Ccre Caulobacter_crescentus_CB15
AEuMe_Mmar Methanococcus_maripaludis_S2 BPrAl_Mlot Mesorhizobium_loti_MAFF303099
AEuMe_Mmaz Methanosarcina_mazei_Go1 BPrAl_Rcon 1 Rickettsia_conorii_Malish_7
AEuMe_Mthe Methanothermobacter_thermautotrophicus_Delta_H BPrAl_Rpal Rhodopseudomonas_palustris_CGA009
AEuTh_Paby Pyrococcus_abyssi_GE5 BPrAl_Rpro 1 Rickettsia_prowazekii_Madrid_E
AEuTh_Pfur Pyrococcus_furiosus_DSM_3638 BPrAl_Rsph Rhodobacter_sphaeroides
AEuTh_Phor Pyrococcus_horikoshii_OT3 BPrAl_Rtyp 1 Rickettsia_typhi_wilmington
AEuTh_Ptor Picrophilus_torridus_DSM_9790 BPrAl_Smel Sinorhizobium_meliloti_1021
AEuTh_Taci Thermoplasma_acidophilum_DSM_1728 BPrAl_Wolb 1 Wolbachia
AEuTh_Tvol Thermoplasma_volcanium_GSS1 BPrBe_Bbro Bordetella_bronchiseptica_RB50
ANaNa_Nequ 1 Nanoarchaeum_equitans_Kin4-M BPrBe_Bpar Bordetella_parapertussis_12822
BAcAc_Blon Bifidobacterium_longum_NCC2705 BPrBe_Bper Bordetella_pertussis_Tohama_I
BAcAc_Cdip Corynebacterium_diphtheriae_NCTC_13129 BPrBe_Cvio Chromobacterium_violaceum_ATCC_12472
BAcAc_Ceff Corynebacterium_efficiens_YS-314 BPrBe_Neur Nitrosomonas_europaea_ATCC_19718
BAcAc_Cglu Corynebacterium_glutamicum_ATCC_13032 BPrBe_Nmen Neisseria_meningitidis_MC58
BAcAc_Lxyl Leifsonia_xyli_ssp._xyli_CTCB07 BPrBe_Rsol Ralstonia_solanacearum_GMI1000
BAcAc_Mavi Mycobacterium_avium_ssp._paratuberculosis_k10 BPrDe_Bbac Bdellovibrio_bacteriovorus_HD100
BAcAc_Mbov Mycobacterium_bovis_AF2122/97 BPrDe_Dpsy Desulfotalea_psychrophila_LSv54
BAcAc_Mlep Mycobacterium_leprae_TN BPrDe_Dvul Desulfovibrio_vulgaris_ssp._vulgaris_Hildenborough
BAcAc_Mtub Mycobacterium_tuberculosis_H37Rv BPrDe_Gsul Geobacter_sulfurreducens_PCA
BAcAc_Pacn Propionibacterium_acnes_KPA171202 BPrEp_Cjej Campylobacter_jejuni_ssp._jejuni_NCTC_11168
BAcAc_Save Streptomyces_avermitilis_MA-4680 BPrEp_Hhep Helicobacter_hepaticus_ATCC_51449
BAcAc_Scoe Streptomyces_coelicolor_A3(2) BPrEp_Hpyl Helicobacter_pylori_26695
BAcAc_Twhi 1 Tropheryma_whipplei_Twist BPrEp_Wsuc Wolinella_succinogenes_DSM_1740
BAcSy_Sthe 1 Symbiobacterium_thermophilum_IAM_14863 BPrGa_Asp. Acinetobacter_sp._ADP1
BAqAq_Aaeo Aquifex_aeolicus_VF5 BPrGa_Baph 1 Buchnera_aphidicola_Bp
BBaBa_Bthe Bacteroides_thetaiotaomicron_VPI-5482 BPrGa_CBlo 1 Candidatus_Blochmannia_floridanus
BBaBa_Pgin Porphyromonas_gingivalis_W83 BPrGa_Cbur Coxiella_burnetii_RSA_493
BChCh_Ccav 1 Chlamydophila_caviae_GPIC BPrGa_Ecar Erwinia_carotovora_ssp._atroseptica_SCRI1043
BChCh_Cmur 1 Chlamydia_muridarum BPrGa_Ecol Escherichia_coli_K12
BChCh_Cpne 1 Chlamydophila_pneumoniae_J138 BPrGa_Hduc Haemophilus_ducreyi_35000HP
BChCh_Ctep Chlorobium_tepidum_TLS BPrGa_Hinf Haemophilus_influenzae_Rd_KW20
BChCh_Ctra 1 Chlamydia_trachomatis_D/UW-3/CX BPrGa_Paer Pseudomonas_aeruginosa_PAO1
BChCh_Psp. 1 Parachlamydia_sp._UWE25 BPrGa_Plum Photorhabdus_luminescens_ssp._laumondii_TTO1
BCyCh_Gvio Gloeobacter_violaceus_PCC_7421 BPrGa_Pmul Pasteurella_multocida_Pm70
BCyCh_Ssp* Synechocystis_sp._PCC_6803 BPrGa_Pput Pseudomonas_putida_KT2440
BCyCh_Ssp. Synechococcus_sp._WH_8102 BPrGa_Psyr Pseudomonas_syringae_pv._tomato_DC3000
BCyCh_Telo Thermosynechococcus_elongatus_BP-1 BPrGa_Sent Salmonella_enterica_ssp._enterica_ser._Typhi_CT18
BCyNo_Nsp. Nostoc_sp._PCC_7120 BPrGa_Sfle Shigella_flexneri_2a_301
BCyPr_Pmar Prochlorococcus_marinus_ssp._marinus_CCMP1375 BPrGa_Sone Shewanella_oneidensis_MR-1
BDeDe_Drad Deinococcus_radiodurans_R1 BPrGa_Styp Salmonella_typhimurium_LT2
BDeDe_Tthe Thermus_thermophilus_HB27 BPrGa_Vcho Vibrio_cholerae_O1_biovar_eltor_N16961
BFiBa_Bant Bacillus_anthracis_Ames BPrGa_Vpar Vibrio_parahaemolyticus_RIMD_2210633
BFiBa_Bcer Bacillus_cereus_ATCC_14579 BPrGa_Vvu* Vibrio_vulnificus_CMCP6
BFiBa_Bhal Bacillus_halodurans_C-125 BPrGa_Vvul Vibrio_vulnificus_YJ016
BFiBa_Bsub Bacillus_subtilis_ssp._subtilis_168 BPrGa_Wglo 1 Wigglesworthia_glossinidia
BFiBa_Bthu Bacillus_thuringiensis_ser._konkukian_97-27 BPrGa_Xaxo Xanthomonas_axonopodis_pv._citri_306
BFiBa_Linn Listeria_innocua_Clip11262 BPrGa_Xcam Xanthomonas_campestris_pv._campestris_ATCC_33913
BFiBa_Lmon Listeria_monocytogenes_EGD-e BPrGa_Xfas Xylella_fastidiosa_9a5c
BFiBa_Oihe Oceanobacillus_iheyensis_HTE831 BPrGa_Ypes Yersinia_pestis_CO92
BFiBa_Saur Staphylococcus_aureus_ssp._aureus_Mu50 BPrGa_Ypse Yersinia_pseudotuberculosis_IP_32953
BFiBa_Sepi Staphylococcus_epidermidis_ATCC_12228 BSpSp_Bbur 1 Borrelia_burgdorferi_B31
BFiCl_Cace Clostridium_acetobutylicum_ATCC_824 BSpSp_Bgar 1 Borrelia_garinii_PBi
BFiCl_Cper Clostridium_perfringens_13 BSpSp_Lint Leptospira_interrogans_ser._Lai_56601
BFiCl_Ctet Clostridium_tetani_E88 BSpSp_Tden 1 Treponema_denticola_ATCC_35405
BFiCl_Tten Thermoanaerobacter_tengcongensis BSpSp_Tpal 1 Treponema_pallidum_ssp._pallidum_Nichols
BFiLa_Efae Enterococcus_faecalis_V583 BThTh_Tmar Thermotoga_maritima_MSB8
BFiLa_Ljoh Lactobacillus_johnsonii_NCC_533 EAlAp_Pfal Plasmodium_falciparum
BFiLa_Llac Lactococcus_lactis_ssp._lactis_Il1403 EAlAp_Pyoe Plasmodium_yoelii_ssp._yoelii
BFiLa_Lpla Lactobacillus_plantarum_WCFS1 EEuKi_Tbru 1 Trypanosoma_brucei
BFiLa_Saga Streptococcus_agalactiae_2603V/R EFuAs_Agos Ashbya_gossypii
BFiLa_Smut Streptococcus_mutans_UA159 EFuAs_Anid Aspergillus_nidulans
BFiLa_Spne Streptococcus_pneumoniae_TIGR4 EFuAs_Calb Candida_albicans
BFiLa_Spy* Streptococcus_pyogenes_M1_GAS EFuAs_Cgla Candida_glabrata
BFiLa_Spyo Streptococcus_pyogenes_MGAS10394 EFuAs_Dhan Debaromyces_hansenii
BFiMo_Mflo 1 Mesoplasma_florum_L1 EFuAs_Fgra Fusarium_graminearum
BFiMo_Mgal 1 Mycoplasma_gallisepticum_R EFuAs_Klac Kluyveromyces_lactis
BFiMo_Mgen 1 Mycoplasma_genitalium_G-37 EFuAs_Kwal Kluyveromyces_waltii
BFiMo_Mmob 1 Mycoplasma_mobile_163K EFuAs_Mgri Magnaporthe_grisea
BFiMo_Mmyc 1 Mycoplasma_mycoides_ssp._mycoides_SC_PG1 EFuAs_Ncra Neurospora_crassa
BFiMo_Mpen 1 Mycoplasma_penetrans_HF-2 EFuAs_Sbay Saccharomyces_bayanus
BFiMo_Mpne 1 Mycoplasma_pneumoniae_M129 EFuAs_Scer Saccharomyces_cerevisiae
BFiMo_Mpul 1 Mycoplasma_pulmonis_UAB_CTIP EFuAs_Smik Saccharomyces_mikatae
BFiMo_Oyel 1 Onion_yellows_phytoplasma_OY-M EFuAs_Spar Saccharomyces_paradoxus
BFiMo_Upar 1 Ureaplasma_parvum_ser._3_ATCC_700970 EFuAs_Spom Schizosaccharomyces_pombe
EFuAs_Ylip Yarrowia_lipolytica
EFuBa_Umay Ustilago_maydis
EFuMi_Ecun 1 Encephalitozoon_cuniculi
EMeAr_Agam Anopheles_gambiae
EMeAr_Dmel Drosophila_melanogaster
EMeCh_Cint Ciona_intestinalis
EMeCh_Drer Danio_rerio
EMeCh_Frub Fugu_rubripes
EMeCh_Ggal Gallus_gallus
EMeCh_Hsap Homo_sapiens
EMeCh_Mmus Mus_musculus
EMeCh_Ptro Pan_troglodytes
EMeCh_Rnor Rattus_norvegicus
EMeCh_Xtro Xenopus_tropicalis
EMeNe_Cbri Caenorhabditis_briggsae
EMeNe_Cele Caenorhabditis_elegans
EMyDi_Ddis Dictyostelium_discoideum
EViSt_Atha Arabidopsis_thaliana
EViSt_Osat Oryza_sativa_ssp._japonica