├── .gitignore ├── C58_Genome.png ├── C58_pTi.png ├── LICENSE ├── README.md ├── beav ├── beav_circos ├── beav_db ├── beav_logo.jpg ├── beav_test ├── beav_workflow.png ├── databases ├── agrobacterium_taxa │ ├── BV1-like__larrymoorei__AF3.10.fna.gz │ ├── BV1-like__rosae__NCPPB_1650.fna.gz │ ├── BV1-like__rubi__W2_73.fna.gz │ ├── BV1-like__skierniewicense__Di1472.fna.gz │ ├── BV1__G13__CFBP_6927.fna.gz │ ├── BV1__G14__39_7.fna.gz │ ├── BV1__G19__ICMP_6402.fna.gz │ ├── BV1__G1__Ach5.fna.gz │ ├── BV1__G20__K599.fna.gz │ ├── BV1__G21__MAFF210266.fna.gz │ ├── BV1__G22__KCJK1736.fna.gz │ ├── BV1__G2__H41.fna.gz │ ├── BV1__G3__SUL3.fna.gz │ ├── BV1__G4__B6.fna.gz │ ├── BV1__G5__CFBP_6626.fna.gz │ ├── BV1__G6__NCPPB_925.fna.gz │ ├── BV1__G7__NCPPB_1641.fna.gz │ ├── BV1__G8__C58.fna.gz │ ├── BV1__G9__YIC_5082.fna.gz │ ├── BV1__arsenijevicii__KFB330.fna.gz │ ├── BV2-like____AB2_73.fna.gz │ ├── BV2____K84.fna.gz │ ├── BV3__ampelinum__S4.fna.gz │ ├── BV3__vitis__NCPPB_3554.fna.gz │ └── R_tumorigenes____B21_90.fna.gz ├── bakta_custom_protein │ ├── Agrobacterium_bakta.faa │ ├── Bradyrhizobium_T3SE_bakta.faa │ ├── GALLS.faa │ ├── Ralstonia_T3SE_currated_prot.fasta.bakta.faa │ ├── Rhodococcus_database.faa │ ├── Sinorhizobium_fredii.tab.bakta.faa │ ├── Streptomyces_database.faa │ ├── T3SS-Hops.txt.filt.bakta.faa │ ├── combined.faa │ ├── symbiosis.bakta.faa │ ├── trbtra.bakta.faa │ └── upp.bakta.faa ├── dif_db.fna ├── more_T-DNA_borders.fna ├── oncogenic_plasmids │ ├── Weisberg2022PhilTransB │ │ ├── A4_ri.sketch │ │ ├── AS1A10_ti.sketch │ │ ├── AS1A6_ti.sketch │ │ ├── AS1B10_ti.sketch │ │ ├── AS1B2_ti.sketch │ │ ├── AS1B4_ti.sketch │ │ ├── AS1B5_ti.sketch │ │ ├── AS1B7_ti.sketch │ │ ├── AS1B8_ti.sketch │ │ ├── AS1B9_ti.sketch │ │ ├── AS1C10_ti.sketch │ │ ├── AS1C1_ti.sketch │ │ ├── AS1C2_ti.sketch │ │ ├── AS1C3_ti.sketch │ │ ├── AS1C4_ti.sketch │ │ ├── AS1C5_ti.sketch │ │ ├── AS1C6_ti.sketch │ │ ├── AS1D10_ti.sketch │ │ ├── AS1D3_ti.sketch │ │ ├── AS1D4_ti.sketch │ │ ├── AS1D6_ti.sketch │ │ ├── AS1D8_ti.sketch │ │ ├── AS1D9_ti.sketch │ │ ├── AS1E10_ti.sketch │ │ ├── AS1E1_ti.sketch │ │ ├── AS1E2_ti.sketch │ │ ├── AS1E3_ti.sketch │ │ ├── AS1E4_ti.sketch │ │ ├── AS1E5_ti.sketch │ │ ├── AS1E6_ti.sketch │ │ ├── AS1E9_ti.sketch │ │ ├── AS1F1_ti.sketch │ │ ├── AS1F2_ti.sketch │ │ ├── AS1F4_ti.sketch │ │ ├── AS1F5_ti.sketch │ │ ├── AS1F6_ti.sketch │ │ ├── AS1F9_ti.sketch │ │ ├── AS1G10_ti.sketch │ │ ├── AS1G1_ti.sketch │ │ ├── AS1G4_ti.sketch │ │ ├── AS1G6_ti.sketch │ │ ├── AS1G9_ti.sketch │ │ ├── AS1H1_ti.sketch │ │ ├── AS1H4_ti.sketch │ │ ├── AS1H5_ti.sketch │ │ ├── AS1H7_ti.sketch │ │ ├── AS1H9_ti.sketch │ │ ├── AS1I1_ti.sketch │ │ ├── AS1I3_ti.sketch │ │ ├── AS1I4_ti.sketch │ │ ├── AS1I5_ti.sketch │ │ ├── AS1I7_ti.sketch │ │ ├── AS1I9_ti.sketch │ │ ├── AS1J1_ti.sketch │ │ ├── AS1J9_ri_ri.sketch │ │ ├── AS1J9_ti_ti.sketch │ │ ├── AS2A10_ti.sketch │ │ ├── AS2A2_ti.sketch │ │ ├── AS2A3_ti.sketch │ │ ├── AS2A4_ti.sketch │ │ ├── AS2A7_ti.sketch │ │ ├── AS2A8_ri.sketch │ │ ├── AS2B10_ti.sketch │ │ ├── AS2B1_ti.sketch │ │ ├── AS2B7_ti.sketch │ │ ├── AS2B8_ri.sketch │ │ ├── AS2C10_ti.sketch │ │ ├── AS2C3_ti.sketch │ │ ├── AS2C7_ti.sketch │ │ ├── AS2C8_ri.sketch │ │ ├── AS2D10_ti.sketch │ │ ├── AS2D2_ti.sketch │ │ ├── AS2D3_ti.sketch │ │ ├── AS2D7_ti.sketch │ │ ├── AS2E10_ti.sketch │ │ ├── AS2E1_ti.sketch │ │ ├── AS2E5_ri.sketch │ │ ├── AS2E7_ti.sketch │ │ ├── AS2F10_ti.sketch │ │ ├── AS2F7_ti.sketch │ │ ├── AS2G10_ti.sketch │ │ ├── AS2G1_ti.sketch │ │ ├── AS2G3_ri.sketch │ │ ├── AS2G7_ti.sketch │ │ ├── AS2H10_ti.sketch │ │ ├── AS2H3_ti.sketch │ │ ├── AS2H4_ti.sketch │ │ ├── AS2H5_ti.sketch │ │ ├── AS2H7_ti.sketch │ │ ├── AS2H9_ti.sketch │ │ ├── AS2I10_ti.sketch │ │ ├── AS2I1_ti.sketch │ │ ├── AS2I3_ri.sketch │ │ ├── AS2I7_ti.sketch │ │ ├── AS2I9_ti.sketch │ │ ├── AS2J10_ti.sketch │ │ ├── AS2J1_ti.sketch │ │ ├── AS2J7_ti.sketch │ │ ├── AS2J9_ti.sketch │ │ ├── AS3A7_ti.sketch │ │ ├── AS3A8_ti.sketch │ │ ├── AS3A9_ti.sketch │ │ ├── AS3B1_ti.sketch │ │ ├── AS3B2_ti.sketch │ │ ├── AS3B3_ti.sketch │ │ ├── AS3B4_ti.sketch │ │ ├── AS3B6_ti.sketch │ │ ├── AS3B7_ti.sketch │ │ ├── AS3B8_ti.sketch │ │ ├── AS3B9_ti.sketch │ │ ├── AS3C1_ti.sketch │ │ ├── AS3C2_ti.sketch │ │ ├── AS3C3_ti.sketch │ │ ├── AS3C4_ti.sketch │ │ ├── AS3C5_ti.sketch │ │ ├── AS3C6_ti.sketch │ │ ├── AS3C7_ti.sketch │ │ ├── AS3C8_ti.sketch │ │ ├── AS3C9_ti.sketch │ │ ├── AS3D1_ti.sketch │ │ ├── AS3D2_ti.sketch │ │ ├── AS3D3_ti.sketch │ │ ├── AS3D4_ti.sketch │ │ ├── AS3D5_ti.sketch │ │ ├── AS3D6_ti.sketch │ │ ├── AS3D7_ti.sketch │ │ ├── AS3D8_ti.sketch │ │ ├── AS3D9_ti.sketch │ │ ├── AS3E6_ti.sketch │ │ ├── AS3E7_ti.sketch │ │ ├── ATCC_15834_ri.sketch │ │ ├── Agrobacterium_arsenijevicii_KFB_330_TypeIa.sketch │ │ ├── Agrobacterium_fabrum_1D132_TypeIb.sketch │ │ ├── Agrobacterium_fabrum_Arqua_RiTypeIII.sketch │ │ ├── Agrobacterium_genomosp_S56_TypeIa.sketch │ │ ├── Agrobacterium_genomosp_TT111_TypeII.sketch │ │ ├── Agrobacterium_larrymoorei_AF3.10___ATCC_51759_Larry.sketch │ │ ├── Agrobacterium_larrymoorei_CFBP5477_TypeIb.sketch │ │ ├── Agrobacterium_rhizogenes_A_1.2.5_TypeIVa.sketch │ │ ├── Agrobacterium_rhizogenes_GBBC3284_RiTypeI.sketch │ │ ├── Agrobacterium_rhizogenes_LMG149_RiTypeII.sketch │ │ ├── Agrobacterium_rhizogenes_LMG150_RiTypeII.sketch │ │ ├── Agrobacterium_rhizogenes_LMG152_RiTypeIII.sketch │ │ ├── Agrobacterium_rhizogenes_LMG63_RiTypeII.sketch │ │ ├── Agrobacterium_rhizogenes_NBRC_13257_RiTypeII.sketch │ │ ├── Agrobacterium_rosae_NCPPB_1650_TypeIb.sketch │ │ ├── Agrobacterium_rubi_TR3___NBRC_13261_TypeIa.sketch │ │ ├── Agrobacterium_salinitolerans_CFBP5507_TypeIa.sketch │ │ ├── Agrobacterium_salinitolerans_GBBC3283_RiTypeI.sketch │ │ ├── Agrobacterium_sp_NCPPB_925_TypeIII.sketch │ │ ├── Agrobacterium_tumefaciens_12D1_TypeIa.sketch │ │ ├── Agrobacterium_tumefaciens_183_TypeIb.sketch │ │ ├── Agrobacterium_tumefaciens_186_TypeIb.sketch │ │ ├── Agrobacterium_tumefaciens_1D1108_TypeIb.sketch │ │ ├── Agrobacterium_tumefaciens_1D1460_TypeIa.sketch │ │ ├── Agrobacterium_tumefaciens_1D1609_TypeII.sketch │ │ ├── Agrobacterium_tumefaciens_A6_TypeII.sketch │ │ ├── Agrobacterium_tumefaciens_CFBP5499_TypeIII.sketch │ │ ├── Agrobacterium_tumefaciens_CFBP5877_TypeIII.sketch │ │ ├── Agrobacterium_tumefaciens_CFBP7129_TypeIa.sketch │ │ ├── Agrobacterium_tumefaciens_F4_TypeIa.sketch │ │ ├── Agrobacterium_tumefaciens_LBA4404_TypeIII.sketch │ │ ├── Agrobacterium_tumefaciens_MAFF210266_RiTypeI.sketch │ │ ├── Agrobacterium_tumefaciens_N2_73_TypeIa.sketch │ │ ├── Agrobacterium_tumefaciens_NCTC13543_TypeII.sketch │ │ ├── Agrobacterium_vitis_AB3_Burr958_ti.sketch │ │ ├── Agrobacterium_vitis_AB4_TypeIVa.sketch │ │ ├── Agrobacterium_vitis_AT6_Burr958_ti.sketch │ │ ├── Agrobacterium_vitis_NW221_TypeV.sketch │ │ ├── Agrobacterium_vitis_Ni1_TypeIVa.sketch │ │ ├── Agrobacterium_vitis_RF2_1_TypeV.sketch │ │ ├── Agrobacterium_vitis_Rr4_TypeIVa.sketch │ │ ├── Agrobacterium_vitis_SF93_TypeV.sketch │ │ ├── Agrobacterium_vitis_Sz1_TypeV.sketch │ │ ├── Agrobacterium_vitis_T1_7_TypeV.sketch │ │ ├── Agrobacterium_vitis_V80_94_TypeV.sketch │ │ ├── Atu_B6_ti.sketch │ │ ├── Avi_NCPPB_3554_ti.sketch │ │ ├── B21_90_ti.sketch │ │ ├── B230_85_ti.sketch │ │ ├── E27B_91_ti.sketch │ │ ├── EML302_ti.sketch │ │ ├── EML303_ti.sketch │ │ ├── EML304_ti.sketch │ │ ├── EML305_ti.sketch │ │ ├── EML459_ti.sketch │ │ ├── EML470_ti.sketch │ │ ├── EML471_ti.sketch │ │ ├── EML474_ti.sketch │ │ ├── EML496_ti.sketch │ │ ├── GC1A3_ti.sketch │ │ ├── JL5029_ti.sketch │ │ ├── JL5161_ti.sketch │ │ ├── JL5162_ti.sketch │ │ ├── JL5163_ti.sketch │ │ ├── JL5165_ti.sketch │ │ ├── JL5166_ti.sketch │ │ ├── JL5167_ti.sketch │ │ ├── JL5170_ti.sketch │ │ ├── JL5172_ti.sketch │ │ ├── JL5175_ti.sketch │ │ ├── JL5177_ti.sketch │ │ ├── JL5180_ti.sketch │ │ ├── JL5181_ti.sketch │ │ ├── JL5182_ri.sketch │ │ ├── JL5183_ti.sketch │ │ ├── JL5187_ti.sketch │ │ ├── JL5191_ti.sketch │ │ ├── JL5198_ti.sketch │ │ ├── JL5200_ti.sketch │ │ ├── JL5201_ti.sketch │ │ ├── JL5216_ti.sketch │ │ ├── JL5217_ti.sketch │ │ ├── JL5222_ti.sketch │ │ ├── JL5226_ti.sketch │ │ ├── JL5231_ti.sketch │ │ ├── JL5234_ti.sketch │ │ ├── JL5238_ti.sketch │ │ ├── JL5240_ti.sketch │ │ ├── JL5241_ti.sketch │ │ ├── JL5246_ti.sketch │ │ ├── JL5249_ti.sketch │ │ ├── JL5250_ti.sketch │ │ ├── JL5252_ti.sketch │ │ ├── JL5253_ti.sketch │ │ ├── JL5254_ti.sketch │ │ ├── JL5257_ti.sketch │ │ ├── JL5258_ti.sketch │ │ ├── JL5268_ri.sketch │ │ ├── JL5274_ti.sketch │ │ ├── JL5275_ti.sketch │ │ ├── JL5276_ti.sketch │ │ ├── JL5280_ti.sketch │ │ ├── JL5281_ti.sketch │ │ ├── JL5286_ti.sketch │ │ ├── K1_93_ti.sketch │ │ ├── K599_ri.sketch │ │ ├── L58_93_ti.sketch │ │ ├── NCIB_8196_ri.sketch │ │ ├── NCPPB3554ti.rotated.sketch │ │ ├── NCPPB_2655_ri.sketch │ │ ├── NCPPB_2657_ri.sketch │ │ ├── Neorhizobium_sp_NCHU2750_TypeIa.sketch │ │ ├── RS2A6_ti.sketch │ │ ├── RS2D4_ti.sketch │ │ ├── RS2E7_ti.sketch │ │ ├── RS2E8_ti.sketch │ │ ├── RS2F7_ti.sketch │ │ ├── RS2H7_ti.sketch │ │ ├── RS2I1_ti.sketch │ │ ├── RS3A6_ti.sketch │ │ ├── p42a_.sketch │ │ ├── pRL7_.sketch │ │ ├── pRi1724.sketch │ │ ├── pRi_26-59.sketch │ │ ├── pTiACH5.sketch │ │ ├── pTiBo542.sketch │ │ ├── pTiC58_ti.sketch │ │ ├── pTiCFBP5477.sketch │ │ ├── pTiEU6.sketch │ │ ├── pTiNCPPB_1641_.sketch │ │ ├── pTiS4_.sketch │ │ ├── pTiSAKURA.sketch │ │ ├── pTi_183.sketch │ │ ├── pTi_186.sketch │ │ ├── pTi_A6.sketch │ │ ├── pTi_AR125.sketch │ │ ├── pTi_C5.7.sketch │ │ ├── pTi_C58PMP90.sketch │ │ ├── pTi_C6.5.sketch │ │ ├── pTi_CFBP1317.sketch │ │ ├── pTi_CFBP1873.sketch │ │ ├── pTi_CFBP1898.sketch │ │ ├── pTi_CFBP1904.sketch │ │ ├── pTi_CFBP1905.sketch │ │ ├── pTi_CFBP1933.sketch │ │ ├── pTi_CFBP1935.sketch │ │ ├── pTi_CFBP2177.sketch │ │ ├── pTi_CFBP2178.sketch │ │ ├── pTi_CFBP2407.sketch │ │ ├── pTi_CFBP2413.sketch │ │ ├── pTi_CFBP2516.sketch │ │ ├── pTi_CFBP2681.sketch │ │ ├── pTi_CFBP2692.sketch │ │ ├── pTi_CFBP2712.sketch │ │ ├── pTi_CFBP2746.sketch │ │ ├── pTi_CFBP2788.sketch │ │ ├── pTi_CFBP296.sketch │ │ ├── pTi_CFBP4423.sketch │ │ ├── pTi_CFBP4424.sketch │ │ ├── pTi_CFBP4442.sketch │ │ ├── pTi_CFBP5473_.sketch │ │ ├── pTi_CFBP5481.sketch │ │ ├── pTi_CFBP5499.sketch │ │ ├── pTi_CFBP5503.sketch │ │ ├── pTi_CFBP5505.sketch │ │ ├── pTi_CFBP5767.sketch │ │ ├── pTi_CFBP6549.sketch │ │ ├── pTi_CFBP7000.sketch │ │ ├── pTi_CFBP7126.sketch │ │ ├── pTi_CFBP7128.sketch │ │ ├── pTi_CFBP7129.sketch │ │ ├── pTi_Chry5.sketch │ │ ├── pTi_DC12-001.sketch │ │ ├── pTi_EHA101.sketch │ │ ├── pTi_GV3101.sketch │ │ ├── pTi_Kerr108.sketch │ │ ├── pTi_Kerr27.sketch │ │ ├── pTi_Sule1.sketch │ │ ├── pTi_T37.sketch │ │ ├── pTi_Tun147.sketch │ │ ├── pTi_Tun151.sketch │ │ ├── pTi_Tun154.sketch │ │ ├── pTi_Tun159.sketch │ │ ├── pTi_Tun176.sketch │ │ ├── pTi_Tun178.sketch │ │ ├── pTi_Tun180.sketch │ │ ├── pTi_Tun183.sketch │ │ ├── pTi_Tun185.sketch │ │ ├── pTi_Tun188.sketch │ │ ├── pTi_Tun198.sketch │ │ ├── pTi_Tun201.sketch │ │ ├── pTi_tumorigenes1078_.sketch │ │ ├── virgenes_A_1.2.5_.sketch │ │ ├── virgenes_BR_10423_.sketch │ │ ├── virgenes_Cherry_2E-2-2_.sketch │ │ ├── virgenes_EML478_.sketch │ │ ├── virgenes_F5.1_.sketch │ │ ├── virgenes_FH14_.sketch │ │ ├── virgenes_MHM7a_.sketch │ │ ├── virgenes_N122_.sketch │ │ ├── virgenes_STM6155_.sketch │ │ └── virgenes_WSM1369_.sketch │ └── burr │ │ ├── CG1000_ti.sketch │ │ ├── CG1001_ti.sketch │ │ ├── CG1002_ti.sketch │ │ ├── CG1003_ti.sketch │ │ ├── CG1005_ti.sketch │ │ ├── CG1013_ti.sketch │ │ ├── CG1016_ti.sketch │ │ ├── CG102_ti.sketch │ │ ├── CG106_ti.sketch │ │ ├── CG107_ti.sketch │ │ ├── CG1080_ti.sketch │ │ ├── CG1081_ti.sketch │ │ ├── CG1082_ti.sketch │ │ ├── CG1083_ti.sketch │ │ ├── CG1084_ti.sketch │ │ ├── CG108_ti.sketch │ │ ├── CG109_ti.sketch │ │ ├── CG1115_ti.sketch │ │ ├── CG1116_ti.sketch │ │ ├── CG1118_ti.sketch │ │ ├── CG115_ti.sketch │ │ ├── CG116_ti.sketch │ │ ├── CG117_vircontigs.sketch │ │ ├── CG128_ti.sketch │ │ ├── CG129_ti.sketch │ │ ├── CG130_ti.sketch │ │ ├── CG132_ti.sketch │ │ ├── CG133_ti.sketch │ │ ├── CG151_ti.sketch │ │ ├── CG156_ti.sketch │ │ ├── CG156_vircontigs.sketch │ │ ├── CG158_ti.sketch │ │ ├── CG169_ti.sketch │ │ ├── CG171_ti.sketch │ │ ├── CG177_ti.sketch │ │ ├── CG180_ti.sketch │ │ ├── CG183_ti.sketch │ │ ├── CG213_ti.sketch │ │ ├── CG218_ti.sketch │ │ ├── CG228_ti.sketch │ │ ├── CG236_ti.sketch │ │ ├── CG406_ti.sketch │ │ ├── CG412_ti.sketch │ │ ├── CG424_ti.sketch │ │ ├── CG435_ti.sketch │ │ ├── CG437_ti.sketch │ │ ├── CG439_ti.sketch │ │ ├── CG442_ti.sketch │ │ ├── CG443_ti.sketch │ │ ├── CG447_ti.sketch │ │ ├── CG448_ti.sketch │ │ ├── CG470_ti.sketch │ │ ├── CG471_ti.sketch │ │ ├── CG474_ti.sketch │ │ ├── CG475_ti.sketch │ │ ├── CG47_ti.sketch │ │ ├── CG485_ti.sketch │ │ ├── CG486_ti.sketch │ │ ├── CG49_ti.sketch │ │ ├── CG513_vircontigs.sketch │ │ ├── CG518_vircontigs.sketch │ │ ├── CG539_vircontigs.sketch │ │ ├── CG543_vircontigs.sketch │ │ ├── CG552_vircontigs.sketch │ │ ├── CG555_vircontigs.sketch │ │ ├── CG562_vircontigs.sketch │ │ ├── CG566_vircontigs.sketch │ │ ├── CG576_vircontigs.sketch │ │ ├── CG577_vircontigs.sketch │ │ ├── CG578_vircontigs.sketch │ │ ├── CG579_vircontigs.sketch │ │ ├── CG608_ti.sketch │ │ ├── CG60_ti.sketch │ │ ├── CG612_ti.sketch │ │ ├── CG619_ti.sketch │ │ ├── CG621_ti.sketch │ │ ├── CG628_ti.sketch │ │ ├── CG653_ti.sketch │ │ ├── CG676_ti.sketch │ │ ├── CG680_ti.sketch │ │ ├── CG693_ti.sketch │ │ ├── CG694_ti.sketch │ │ ├── CG696_ti.sketch │ │ ├── CG714_ti.sketch │ │ ├── CG724_ti.sketch │ │ ├── CG747_ti.sketch │ │ ├── CG747_vircontigs.sketch │ │ ├── CG78_ti.sketch │ │ ├── CG81_ti.sketch │ │ ├── CG88_ti.sketch │ │ ├── CG94_ti.sketch │ │ ├── CG957_ti.sketch │ │ ├── CG958_ti.sketch │ │ ├── CG966_ti.sketch │ │ ├── CG967_ti.sketch │ │ ├── CG968_ti.sketch │ │ ├── CG969_ti.sketch │ │ ├── CG970_ti.sketch │ │ ├── CG976_ti.sketch │ │ ├── CG987_ti.sketch │ │ ├── CG988_ti.sketch │ │ ├── CG989_ti.sketch │ │ ├── CG990_ti.sketch │ │ ├── CG997_ti.sketch │ │ └── CG998_ti.sketch └── oriT_db.fna ├── models ├── T-DNA_leftborder.hmm ├── T-DNA_rightborder.hmm ├── TIGR01646.1.hmm ├── TIGR03361.1.hmm ├── dif.hmm ├── nodbox.hmm ├── overdrive.hmm └── ttsbox.hmm ├── scripts ├── antismash_genbanks_to_table.py ├── beav_circos.py ├── beav_circos.sh ├── beav_oncogenes.py ├── check_agrobacteria_biovar.sh ├── check_operon_mapper_status.sh ├── combine_annotations.py ├── convert_gbff.py ├── find_dif.sh ├── find_oriT.sh ├── identify_Ti_Ri_plasmid_contigs.sh ├── identify_vgrG_clusters.sh ├── make_summary.sh ├── makegembase.py ├── process_IntegronFinder.sh ├── run_GapMind_aa_carbon.sh ├── run_TIGER2.sh ├── submit_operon-mapper_job.py ├── subset_cds_genbank.py └── tiger.patch ├── software └── README.md └── test_data ├── C58db ├── Agrobacterium_fabrum_C58.fna ├── Agrobacterium_fabrum_C58.fna.ndb ├── Agrobacterium_fabrum_C58.fna.nhr ├── Agrobacterium_fabrum_C58.fna.nin ├── Agrobacterium_fabrum_C58.fna.njs ├── Agrobacterium_fabrum_C58.fna.not ├── Agrobacterium_fabrum_C58.fna.nsq ├── Agrobacterium_fabrum_C58.fna.ntf └── Agrobacterium_fabrum_C58.fna.nto └── test.fna /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weisberglab/beav/HEAD/.gitignore -------------------------------------------------------------------------------- /C58_Genome.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weisberglab/beav/HEAD/C58_Genome.png -------------------------------------------------------------------------------- /C58_pTi.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/weisberglab/beav/HEAD/C58_pTi.png -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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