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NCBI has a
taxonomy
tool for prokaryotic genomes.
The ATGC database provides a
perfect source of input genomes to use for our project, which they
call Alignable Tight Genomic Clusters. This is probably a better
starting point than my rather ad hoc list below.
Listed below are some sample families of bacterial genomes on which you might
experiment. All are available from
NCBI's Microbial FTP
directory.
Acinetobacter_baumannii_AB0057
Acinetobacter_baumannii_AB307_0294
Acinetobacter_baumannii_ACICU
Acinetobacter_baumannii_ATCC_17978
Acinetobacter_baumannii_AYE
Acinetobacter_baumannii_SDF
Actinobacillus_pleuropneumoniae_L20
Actinobacillus_pleuropneumoniae_serovar_3_JL03
Actinobacillus_pleuropneumoniae_serovar_7_AP76
Actinobacillus_succinogenes_130Z
Bacillus_amyloliquefaciens_FZB42
Bacillus_anthracis_Ames
Bacillus_anthracis_Ames_0581
Bacillus_anthracis_str_Sterne
Bacillus_cereus_AH187
Bacillus_cereus_AH820
Bacillus_cereus_ATCC14579
Bacillus_cereus_ATCC_10987
Bacillus_cereus_B4264
Bacillus_cereus_G9842
Bacillus_cereus_Q1
Bacillus_cereus_ZK
Bacillus_cereus_cytotoxis_NVH_391-98
Bacillus_clausii_KSM-K16
Bacillus_halodurans
Bacillus_licheniformis_ATCC_14580
Bacillus_licheniformis_DSM_13
Bacillus_pumilus_SAFR-032
Bacillus_subtilis
Bacillus_thuringiensis_Al_Hakam
Bacillus_thuringiensis_konkukian
Bacillus_weihenstephanensis_KBAB4
Buchnera_aphidicola
Buchnera_aphidicola_5A__Acyrthosiphon_pisum_
Buchnera_aphidicola_Cc_Cinara_cedri
Buchnera_aphidicola_Sg
Buchnera_aphidicola_Tuc7__Acyrthosiphon_pisum_
Burkholderia_383
Burkholderia_ambifaria_MC40_6
Burkholderia_cenocepacia_AU_1054
Burkholderia_cenocepacia_HI2424
Burkholderia_cenocepacia_J2315
Burkholderia_cenocepacia_MC0_3
Burkholderia_cepacia_AMMD
Burkholderia_mallei_ATCC_23344
Burkholderia_mallei_NCTC_10229
Burkholderia_mallei_NCTC_10247
Burkholderia_mallei_SAVP1
Burkholderia_multivorans_ATCC_17616_JGI
Burkholderia_multivorans_ATCC_17616_Tohoku
Burkholderia_phymatum_STM815
Burkholderia_phytofirmans_PsJN
Burkholderia_pseudomallei_1106a
Burkholderia_pseudomallei_1710b
Burkholderia_pseudomallei_668
Burkholderia_pseudomallei_K96243
Burkholderia_thailandensis_E264
Burkholderia_vietnamiensis_G4
Burkholderia_xenovorans_LB400
Campylobacter_concisus_13826
Campylobacter_curvus_525_92
Campylobacter_fetus_82-40
Campylobacter_hominis_ATCC_BAA-381
Campylobacter_jejuni
Campylobacter_jejuni_81-176
Campylobacter_jejuni_81116
Campylobacter_jejuni_RM1221
Campylobacter_jejuni_doylei_269_97
Campylobacter_lari_RM2100
Chlamydia_muridarum
Chlamydia_trachomatis
Chlamydia_trachomatis_434_Bu
Chlamydia_trachomatis_A_HAR-13
Chlamydia_trachomatis_L2b_UCH_1_proctitis
Chlamydophila_abortus_S26_3
Chlamydophila_caviae
Chlamydophila_felis_Fe_C-56
Chlamydophila_pneumoniae_AR39
Chlamydophila_pneumoniae_CWL029
Chlamydophila_pneumoniae_J138
Chlamydophila_pneumoniae_TW_183
Clostridium_acetobutylicum
Clostridium_beijerinckii_NCIMB_8052
Clostridium_botulinum_A
Clostridium_botulinum_A3_Loch_Maree
Clostridium_botulinum_A_ATCC_19397
Clostridium_botulinum_A_Hall
Clostridium_botulinum_B1_Okra
Clostridium_botulinum_B_Eklund_17B
Clostridium_botulinum_E3_Alaska_E43
Clostridium_botulinum_F_Langeland
Clostridium_cellulolyticum_H10
Clostridium_difficile_630
Clostridium_kluyveri_DSM_555
Clostridium_kluyveri_NBRC_12016
Clostridium_novyi_NT
Clostridium_perfringens
Clostridium_perfringens_ATCC_13124
Clostridium_perfringens_SM101
Clostridium_phytofermentans_ISDg
Clostridium_tetani_E88
Clostridium_thermocellum_ATCC_27405
Coxiella_burnetii
Coxiella_burnetii_CbuG_Q212
Coxiella_burnetii_CbuK_Q154
Coxiella_burnetii_Dugway_7E9-12
Coxiella_burnetii_RSA_331
Escherichia_coli_0127_H6_E2348_69
Escherichia_coli_536
Escherichia_coli_55989
Escherichia_coli_APEC_O1
Escherichia_coli_CFT073
Escherichia_coli_C_ATCC_8739
Escherichia_coli_E24377A
Escherichia_coli_ED1a
Escherichia_coli_HS
Escherichia_coli_IAI1
Escherichia_coli_IAI39
Escherichia_coli_K_12_substr__DH10B
Escherichia_coli_K_12_substr__MG1655
Escherichia_coli_K_12_substr__W3110
Escherichia_coli_O157H7
Escherichia_coli_O157H7_EDL933
Escherichia_coli_O157_H7_EC4115
Escherichia_coli_S88
Escherichia_coli_SE11
Escherichia_coli_SMS_3_5
Escherichia_coli_UMN026
Escherichia_coli_UTI89
Francisella_philomiragia_ATCC_25017
Francisella_tularensis_FSC_198
Francisella_tularensis_WY96-3418
Francisella_tularensis_holarctica
Francisella_tularensis_holarctica_FTA
Francisella_tularensis_holarctica_OSU18
Francisella_tularensis_mediasiatica_FSC147
Francisella_tularensis_novicida_U112
Francisella_tularensis_tularensis
Geobacter_metallireducens_GS-15
Geobacter_sulfurreducens
Geobacter_uraniumreducens_Rf4
Haemophilus_ducreyi_35000HP
Haemophilus_influenzae
Haemophilus_influenzae_86_028NP
Haemophilus_influenzae_PittEE
Haemophilus_influenzae_PittGG
Haemophilus_parasuis_SH0165
Haemophilus_somnus_129PT
Haemophilus_somnus_2336
Helicobacter_hepaticus
Helicobacter_pylori_26695
Helicobacter_pylori_G27
Helicobacter_pylori_HPAG1
Helicobacter_pylori_J99
Helicobacter_pylori_P12
Helicobacter_pylori_Shi470
Lactobacillus_acidophilus_NCFM
Lactobacillus_brevis_ATCC_367
Lactobacillus_casei
Lactobacillus_casei_ATCC_334
Lactobacillus_delbrueckii_bulgaricus
Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365
Lactobacillus_fermentum_IFO_3956
Lactobacillus_gasseri_ATCC_33323
Lactobacillus_helveticus_DPC_4571
Lactobacillus_johnsonii_NCC_533
Lactobacillus_plantarum
Lactobacillus_reuteri_DSM_20016
Lactobacillus_reuteri_F275_Kitasato
Lactobacillus_sakei_23K
Lactobacillus_salivarius_UCC118
Legionella_pneumophila_Corby
Legionella_pneumophila_Lens
Legionella_pneumophila_Paris
Legionella_pneumophila_Philadelphia_1
Methanococcus_aeolicus_Nankai-3
Methanococcus_jannaschii
Methanococcus_maripaludis_C5
Methanococcus_maripaludis_C6
Methanococcus_maripaludis_C7
Methanococcus_maripaludis_S2
Methanococcus_vannielii_SB
Mycobacterium_JLS
Mycobacterium_KMS
Mycobacterium_MCS
Mycobacterium_abscessus_ATCC_19977T
Mycobacterium_avium_104
Mycobacterium_avium_paratuberculosis
Mycobacterium_bovis
Mycobacterium_bovis_BCG_Pasteur_1173P2
Mycobacterium_bovis_BCG_Tokyo_172
Mycobacterium_gilvum_PYR-GCK
Mycobacterium_leprae
Mycobacterium_leprae_Br4923
Mycobacterium_marinum_M
Mycobacterium_smegmatis_MC2_155
Mycobacterium_tuberculosis_CDC1551
Mycobacterium_tuberculosis_F11
Mycobacterium_tuberculosis_H37Ra
Mycobacterium_tuberculosis_H37Rv
Mycobacterium_ulcerans_Agy99
Mycobacterium_vanbaalenii_PYR-1
Neisseria_gonorrhoeae_FA_1090
Neisseria_gonorrhoeae_NCCP11945
Neisseria_meningitidis_053442
Neisseria_meningitidis_FAM18
Neisseria_meningitidis_MC58
Neisseria_meningitidis_Z2491
Prochlorococcus_marinus_AS9601
Prochlorococcus_marinus_CCMP1375
Prochlorococcus_marinus_MED4
Prochlorococcus_marinus_MIT9313
Prochlorococcus_marinus_MIT_9211
Prochlorococcus_marinus_MIT_9215
Prochlorococcus_marinus_MIT_9301
Prochlorococcus_marinus_MIT_9303
Prochlorococcus_marinus_MIT_9312
Prochlorococcus_marinus_MIT_9515
Prochlorococcus_marinus_NATL1A
Prochlorococcus_marinus_NATL2A
Pseudomonas_aeruginosa
Pseudomonas_aeruginosa_LESB58
Pseudomonas_aeruginosa_PA7
Pseudomonas_aeruginosa_UCBPP-PA14
Pseudomonas_entomophila_L48
Pseudomonas_fluorescens_Pf-5
Pseudomonas_fluorescens_Pf0_1
Pseudomonas_mendocina_ymp
Pseudomonas_putida_F1
Pseudomonas_putida_GB_1
Pseudomonas_putida_KT2440
Pseudomonas_putida_W619
Pseudomonas_stutzeri_A1501
Pseudomonas_syringae_phaseolicola_1448A
Pseudomonas_syringae_pv_B728a
Pseudomonas_syringae_tomato_DC3000
Rhodobacter_sphaeroides_2_4_1
Rhodobacter_sphaeroides_ATCC_17025
Rhodobacter_sphaeroides_ATCC_17029
Rhodobacter_sphaeroides_KD131
Rhodopseudomonas_palustris_BisA53
Rhodopseudomonas_palustris_BisB18
Rhodopseudomonas_palustris_BisB5
Rhodopseudomonas_palustris_CGA009
Rhodopseudomonas_palustris_HaA2
Rhodopseudomonas_palustris_TIE_1
Salmonella_enterica_Choleraesuis
Salmonella_enterica_Paratypi_ATCC_9150
Salmonella_enterica_arizonae_serovar_62_z4_z23__
Salmonella_enterica_serovar_Agona_SL483
Salmonella_enterica_serovar_Dublin_CT_02021853
Salmonella_enterica_serovar_Enteritidis_P125109
Salmonella_enterica_serovar_Gallinarum_287_91
Salmonella_enterica_serovar_Heidelberg_SL476
Salmonella_enterica_serovar_Newport_SL254
Salmonella_enterica_serovar_Paratyphi_A_AKU_12601
Salmonella_enterica_serovar_Paratyphi_B_SPB7
Salmonella_enterica_serovar_Paratyphi_C_RKS4594
Salmonella_enterica_serovar_Schwarzengrund_CVM19633
Salmonella_enterica_serovar_Typhi_Ty2
Salmonella_typhi
Salmonella_typhimurium_LT2
Shigella_boydii_CDC_3083_94
Shigella_boydii_Sb227
Shigella_dysenteriae
Shigella_flexneri_2a
Shigella_flexneri_2a_2457T
Shigella_flexneri_5_8401
Shigella_sonnei_Ss046
Staphylococcus_aureus_COL
Staphylococcus_aureus_JH1
Staphylococcus_aureus_JH9
Staphylococcus_aureus_MW2
Staphylococcus_aureus_Mu3
Staphylococcus_aureus_Mu50
Staphylococcus_aureus_N315
Staphylococcus_aureus_NCTC_8325
Staphylococcus_aureus_Newman
Staphylococcus_aureus_RF122
Staphylococcus_aureus_USA300
Staphylococcus_aureus_USA300_TCH1516
Staphylococcus_aureus_aureus_MRSA252
Staphylococcus_aureus_aureus_MSSA476
Staphylococcus_carnosus_TM300
Staphylococcus_epidermidis_ATCC_12228
Staphylococcus_epidermidis_RP62A
Staphylococcus_haemolyticus
Staphylococcus_saprophyticus
Streptococcus_agalactiae_2603
Streptococcus_agalactiae_A909
Streptococcus_agalactiae_NEM316
Streptococcus_equi_zooepidemicus_MGCS10565
Streptococcus_gordonii_Challis_substr_CH1
Streptococcus_mutans
Streptococcus_pneumoniae_ATCC_700669
Streptococcus_pneumoniae_CGSP14
Streptococcus_pneumoniae_D39
Streptococcus_pneumoniae_G54
Streptococcus_pneumoniae_Hungary19A_6
Streptococcus_pneumoniae_R6
Streptococcus_pneumoniae_TIGR4
Streptococcus_pyogenes_M1_GAS
Streptococcus_pyogenes_MGAS10270
Streptococcus_pyogenes_MGAS10394
Streptococcus_pyogenes_MGAS10750
Streptococcus_pyogenes_MGAS2096
Streptococcus_pyogenes_MGAS315
Streptococcus_pyogenes_MGAS5005
Streptococcus_pyogenes_MGAS6180
Streptococcus_pyogenes_MGAS8232
Streptococcus_pyogenes_MGAS9429
Streptococcus_pyogenes_Manfredo
Streptococcus_pyogenes_NZ131
Streptococcus_pyogenes_SSI-1
Streptococcus_sanguinis_SK36
Streptococcus_suis_05ZYH33
Streptococcus_suis_98HAH33
Streptococcus_thermophilus_CNRZ1066
Streptococcus_thermophilus_LMD-9
Streptococcus_thermophilus_LMG_18311
Streptococcus_uberis_0140J
Xanthomonas_campestris_8004
Xanthomonas_campestris_ATCC_33913
Xanthomonas_campestris_B100
Xanthomonas_campestris_vesicatoria_85-10
Xanthomonas_citri
Xanthomonas_oryzae_KACC10331
Xanthomonas_oryzae_MAFF_311018
Xanthomonas_oryzae_PXO99A
Xylella_fastidiosa
Xylella_fastidiosa_M12
Xylella_fastidiosa_M23
Xylella_fastidiosa_Temecula1
Yersinia_enterocolitica_8081
Yersinia_pestis_Angola
Yersinia_pestis_Antiqua
Yersinia_pestis_CO92
Yersinia_pestis_KIM
Yersinia_pestis_Nepal516
Yersinia_pestis_Pestoides_F
Yersinia_pestis_biovar_Microtus_91001
Yersinia_pseudotuberculosis_IP32953
Yersinia_pseudotuberculosis_IP_31758
Yersinia_pseudotuberculosis_PB1_
Yersinia_pseudotuberculosis_YPIII
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