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Smalt_AA1_3/

Smalt_AB550_0/

Smalt_AB550_1/

Smalt_AB550_2/

Smalt_AB550_3/

Smalt_AB550_4/

Smalt_CF13_0/

Smalt_CF13_2/

Smalt_CF13_3/

Smalt_CPBW01_0/

Smalt_CPBW01_1/

Smalt_CSM2_0/

Smalt_CSM2_1/

Smalt_Col1_0/

Smalt_Col1_1/

Smalt_Col1_2/

Smalt_D457_0/

Smalt_D457_1/

Smalt_D457_2/

Smalt_D457_4/

Smalt_DHHJ_1/

Smalt_DHHJ_3/

Smalt_FDAARGOS_1044_1/

Smalt_FDAARGOS_325_0/

Smalt_FDAARGOS_325_1/

Smalt_FDAARGOS_325_3/

Smalt_FDAARGOS_325_4/

Smalt_FDAARGOS_507_0/

Smalt_FDAARGOS_507_1/

Smalt_FDAARGOS_507_2/

Smalt_FDAARGOS_507_3/

Smalt_FDAARGOS_649_2/

Smalt_FDAARGOS_649_3/

Smalt_FDAARGOS_649_4/

Smalt_FDAARGOS_92_2/

Smalt_FDAARGOS_92_3/

Smalt_FDAARGOS_92_4/

Smalt_ICU331_0/

Smalt_ICU331_2/

Smalt_ICU331_3/

Smalt_ICU331_4/

Smalt_ISMMS2_0/

Smalt_ISMMS2_1/

Smalt_ISMMS2_2/

Smalt_ISMMS2_3/

Smalt_ISMMS2_4/

Smalt_ISMMS3_0/

Smalt_ISMMS3_4/

Smalt_JV3_0/

Smalt_JV3_1/

Smalt_JV3_2/

Smalt_JV3_3/

Smalt_JV3_4/

Smalt_K279a_0/

Smalt_K279a_2/

Smalt_K279a_3/

Smalt_K279a_4/

Smalt_KMM349_1/

Smalt_KMM349_2/

Smalt_KMM349_3/

Smalt_KMM349_4/

Smalt_MER1_2/

Smalt_NCTC10257_1/

Smalt_NCTC10257_2/

Smalt_NCTC10257_3/

Smalt_NCTC10257_4/

Smalt_NCTC10258_0/

Smalt_NCTC10258_1/

Smalt_NCTC10258_3/

Smalt_NCTC10258_4/

Smalt_NCTC10259_0/

Smalt_NCTC10259_1/

Smalt_NCTC10259_2/

Smalt_NCTC10498_0/

Smalt_NCTC10498_2/

Smalt_NCTC10498_3/

Smalt_NCTC10498_4/

Smalt_NCTC13014_0/

Smalt_NCTC13014_1/

Smalt_NCTC13014_4/

Smalt_NEB515_0/

Smalt_NEB515_2/

Smalt_O1_1/

Smalt_O1_2/

Smalt_O1_3/

Smalt_OUC_Est10_1/

Smalt_OUC_Est10_2/

Smalt_OUC_Est10_3/

Smalt_OUC_Est10_4/

Smalt_PEG-141_0/

Smalt_PEG-141_1/

Smalt_PEG-141_2/

Smalt_PEG-141_3/

Smalt_PEG-141_4/

Smalt_PEG-173_0/

Smalt_PEG-173_1/

Smalt_PEG-173_2/

Smalt_PEG-173_4/

Smalt_PEG-305_0/

Smalt_PEG-305_3/

Smalt_PEG-305_4/

Smalt_PEG-390_0/

Smalt_PEG-42_1/

Smalt_PEG-42_2/

Smalt_PEG-42_3/

Smalt_PEG-42_4/

Smalt_PEG-68_0/

Smalt_PEG-68_1/

Smalt_PEG-68_2/

Smalt_PEG-68_3/

Smalt_PEG-68_4/

Smalt_R551-3_1/

Smalt_R551-3_3/

Smalt_R551-3_4/

Smalt_SJTH1_1/

Smalt_SJTH1_2/

Smalt_SJTH1_3/

Smalt_SJTL3_1/

Smalt_SJTL3_4/

Smalt_SM866_0/

Smalt_SM866_1/

Smalt_Sm53_0/

Smalt_Sm53_2/

Smalt_Sm53_3/

Smalt_Sm53_4/

Smalt_SoD9b_1/

Smalt_SoD9b_3/

Smalt_SoD9b_4/

Smalt_T50-20_2/

Smalt_T50-20_3/

Smalt_U5_0/

Smalt_U5_1/

Smalt_W18_0/

Smalt_W18_1/

Smalt_W18_2/

Smalt_W18_3/

Smalt_WP1-W18-CRE-01_0/

Smalt_WP1-W18-CRE-01_2/

Smalt_WP1-W18-CRE-01_3/

Smalt_X28_1/

Smalt_X28_2/

Smalt_sm-RA9_1/

Smalt_sm-RA9_4/

Smalt_sm454_2/

Smalt_sm454_3/

Smalt_sm454_4/

blastout/

Smalt_AA1_0

Smalt_AA1_1

Smalt_AA1_2

Smalt_AA1_4

Smalt_CF13_1

Smalt_CF13_4

Smalt_CPBW01_2

Smalt_CPBW01_3

Smalt_CPBW01_4

Smalt_CSM2_2

Smalt_CSM2_3

Smalt_CSM2_4

Smalt_Col1_3

Smalt_Col1_4

Smalt_D457_3

Smalt_DHHJ_0

Smalt_DHHJ_2

Smalt_DHHJ_4

Smalt_FDAARGOS_1044_0

Smalt_FDAARGOS_1044_2

Smalt_FDAARGOS_1044_3

Smalt_FDAARGOS_1044_4

Smalt_FDAARGOS_325_2

Smalt_FDAARGOS_507_4

Smalt_FDAARGOS_649_0

Smalt_FDAARGOS_649_1

Smalt_FDAARGOS_92_0

Smalt_FDAARGOS_92_1

Smalt_ICU331_1

Smalt_ISMMS2R_0

Smalt_ISMMS2R_1

Smalt_ISMMS2R_2

Smalt_ISMMS2R_3

Smalt_ISMMS2R_4

Smalt_ISMMS3.overrep

Smalt_ISMMS3.wfr

Smalt_ISMMS3_1

Smalt_ISMMS3_2

Smalt_ISMMS3_3

Smalt_K279a_1

Smalt_KMM349_0

Smalt_MER1_0

Smalt_MER1_1

Smalt_MER1_3

Smalt_MER1_4

Smalt_NCTC10257_0

Smalt_NCTC10258_2

Smalt_NCTC10259_3

Smalt_NCTC10259_4

Smalt_NCTC10498_1

Smalt_NCTC13014_2

Smalt_NCTC13014_3

Smalt_NEB515_1

Smalt_NEB515_3

Smalt_NEB515_4

Smalt_O1_0

Smalt_O1_4

Smalt_OUC_Est10_0

Smalt_PEG-173_3

Smalt_PEG-305_1

Smalt_PEG-305_2

Smalt_PEG-390_1

Smalt_PEG-390_2

Smalt_PEG-390_3

Smalt_PEG-390_4

Smalt_PEG-42_0

Smalt_R551-3_0

Smalt_R551-3_2

Smalt_SJTH1_0

Smalt_SJTH1_4

Smalt_SJTL3_0

Smalt_SJTL3_2

Smalt_SJTL3_3

Smalt_SKK55_0

Smalt_SKK55_1

Smalt_SKK55_2

Smalt_SKK55_3

Smalt_SKK55_4

Smalt_SM866_2

Smalt_SM866_3

Smalt_SM866_4

Smalt_Sm53_1

Smalt_SoD9b_0

Smalt_SoD9b_2

Smalt_T50-20_0

Smalt_T50-20_1

Smalt_T50-20_4

Smalt_U5_2

Smalt_U5_3

Smalt_U5_4

Smalt_W18_4

Smalt_WP1-W18-CRE-01_1

Smalt_WP1-W18-CRE-01_4

Smalt_X28_0

Smalt_X28_3

Smalt_X28_4

Smalt_sm-RA9_0

Smalt_sm-RA9_2

Smalt_sm-RA9_3

Smalt_sm454_0

Smalt_sm454_1

groupSeedSequences

maxREPIN_0.txt

maxREPIN_1.txt

maxREPIN_2.txt

maxREPIN_3.txt

maxREPIN_4.txt

presAbs_0.txt

presAbs_1.txt

presAbs_2.txt

presAbs_3.txt

presAbs_4.txt

rarefan.log

raytAln.phy

raytAln.phy_phyml_stats.txt

raytAln.phy_phyml_tree.txt

rayt_Smalt_AA1.gff3

rayt_Smalt_AA1.tab

rayt_Smalt_AB550.gff3

rayt_Smalt_AB550.tab

rayt_Smalt_CF13.gff3

rayt_Smalt_CF13.tab

rayt_Smalt_CPBW01.gff3

rayt_Smalt_CPBW01.tab

rayt_Smalt_CSM2.gff3

rayt_Smalt_CSM2.tab

rayt_Smalt_Col1.gff3

rayt_Smalt_Col1.tab

rayt_Smalt_D457.gff3

rayt_Smalt_D457.tab

rayt_Smalt_DHHJ.gff3

rayt_Smalt_DHHJ.tab

rayt_Smalt_FDAARGOS_1044.gff3

rayt_Smalt_FDAARGOS_1044.tab

rayt_Smalt_FDAARGOS_325.gff3

rayt_Smalt_FDAARGOS_325.tab

rayt_Smalt_FDAARGOS_507.gff3

rayt_Smalt_FDAARGOS_507.tab

rayt_Smalt_FDAARGOS_649.gff3

rayt_Smalt_FDAARGOS_649.tab

rayt_Smalt_FDAARGOS_92.gff3

rayt_Smalt_FDAARGOS_92.tab

rayt_Smalt_ICU331.gff3

rayt_Smalt_ICU331.tab

rayt_Smalt_ISMMS2.gff3

rayt_Smalt_ISMMS2.tab

rayt_Smalt_ISMMS2R.gff3

rayt_Smalt_ISMMS2R.tab

rayt_Smalt_ISMMS3.gff3

rayt_Smalt_ISMMS3.tab

rayt_Smalt_JV3.gff3

rayt_Smalt_JV3.tab

rayt_Smalt_K279a.gff3

rayt_Smalt_K279a.tab

rayt_Smalt_KMM349.gff3

rayt_Smalt_KMM349.tab

rayt_Smalt_MER1.gff3

rayt_Smalt_MER1.tab

rayt_Smalt_NCTC10257.gff3

rayt_Smalt_NCTC10257.tab

rayt_Smalt_NCTC10258.gff3

rayt_Smalt_NCTC10258.tab

rayt_Smalt_NCTC10259.gff3

rayt_Smalt_NCTC10259.tab

rayt_Smalt_NCTC10498.gff3

rayt_Smalt_NCTC10498.tab

rayt_Smalt_NCTC13014.gff3

rayt_Smalt_NCTC13014.tab

rayt_Smalt_NEB515.gff3

rayt_Smalt_NEB515.tab

rayt_Smalt_O1.gff3

rayt_Smalt_O1.tab

rayt_Smalt_OUC_Est10.gff3

rayt_Smalt_OUC_Est10.tab

rayt_Smalt_PEG-141.gff3

rayt_Smalt_PEG-141.tab

rayt_Smalt_PEG-173.gff3

rayt_Smalt_PEG-173.tab

rayt_Smalt_PEG-305.gff3

rayt_Smalt_PEG-305.tab

rayt_Smalt_PEG-390.gff3

rayt_Smalt_PEG-390.tab

rayt_Smalt_PEG-42.gff3

rayt_Smalt_PEG-42.tab

rayt_Smalt_PEG-68.gff3

rayt_Smalt_PEG-68.tab

rayt_Smalt_R551-3.gff3

rayt_Smalt_R551-3.tab

rayt_Smalt_SJTH1.gff3

rayt_Smalt_SJTH1.tab

rayt_Smalt_SJTL3.gff3

rayt_Smalt_SJTL3.tab

rayt_Smalt_SKK55.gff3

rayt_Smalt_SKK55.tab

rayt_Smalt_SM866.gff3

rayt_Smalt_SM866.tab

rayt_Smalt_Sm53.gff3

rayt_Smalt_Sm53.tab

rayt_Smalt_SoD9b.gff3

rayt_Smalt_SoD9b.tab

rayt_Smalt_T50-20.gff3

rayt_Smalt_T50-20.tab

rayt_Smalt_U5.gff3

rayt_Smalt_U5.tab

rayt_Smalt_W18.gff3

rayt_Smalt_W18.tab

rayt_Smalt_WP1-W18-CRE-01.gff3

rayt_Smalt_WP1-W18-CRE-01.tab

rayt_Smalt_X28.gff3

rayt_Smalt_X28.tab

rayt_Smalt_sm-RA9.gff3

rayt_Smalt_sm-RA9.tab

rayt_Smalt_sm454.gff3

rayt_Smalt_sm454.tab

rayt_align.log

rayt_phylo.log

readme.md

repin_rayt_association.txt

repin_rayt_association.txt.fas

repin_rayt_association_byREPIN.txt

results.txt

tmptree.dist

tmptree.nwk

tree.log

yafM_relatives.fna

zip.log