README.md
pyproject.toml
config/defaults.yaml
data/manifest.json
data/classifier/concat_kept_columns.txt
data/classifier/epa_model.model
data/classifier/marker_files.tsv
data/classifier/marker_order.tsv
data/classifier/placement_neighbors.tsv
data/classifier/raxml_epa_edge_map.source.json
data/classifier/raxml_epa_edge_map.tsv
data/classifier/reference_genomes.tsv
data/classifier/reference_taxonomy.tsv
data/classifier/sar11.concatenated_trimmed.faa.raxml.bestModel
data/classifier/sar11.concatenated_trimmed.faa.raxml.bestTree
data/classifier/sar11.partitions.txt
data/classifier/trusted_assignment_reference.tsv
data/classifier/trusted_nodes.tsv
data/classifier/hmm/genes.hmm
data/classifier/msa/sar11.concatenated.faa
data/classifier/msa/sar11.concatenated_trimmed.faa
data/classifier/msa/alignments/ATP_synthase_F0_sub_a.aln.faa
data/classifier/msa/alignments/ApbC.aln.faa
data/classifier/msa/alignments/Beta_lactamase_like_protein.aln.faa
data/classifier/msa/alignments/BolA_family_protein.aln.faa
data/classifier/msa/alignments/DNA_polymerase_I.aln.faa
data/classifier/msa/alignments/DnaA_2.aln.faa
data/classifier/msa/alignments/GrpE.aln.faa
data/classifier/msa/alignments/Holliday_junction_resolvase_like.aln.faa
data/classifier/msa/alignments/HslV.aln.faa
data/classifier/msa/alignments/MraW.aln.faa
data/classifier/msa/alignments/NifU.aln.faa
data/classifier/msa/alignments/PDT.aln.faa
data/classifier/msa/alignments/RNA_polymerase_sub_a.aln.faa
data/classifier/msa/alignments/Ribonuclease_3.aln.faa
data/classifier/msa/alignments/Ribosome_binding_factor_A.aln.faa
data/classifier/msa/alignments/Tim44.aln.faa
data/classifier/msa/alignments/TraR.aln.faa
data/classifier/msa/alignments/UDP_N_AEPG_reductase.aln.faa
data/classifier/msa/alignments/UDP_N_AGPPlase.aln.faa
data/classifier/msa/alignments/YajC.aln.faa
data/classifier/msa/alignments/YidC.aln.faa
data/classifier/msa/alignments/acpS.aln.faa
data/classifier/msa/alignments/acyl_carrier_protein.aln.faa
data/classifier/msa/alignments/afg1_family_ATPase.aln.faa
data/classifier/msa/alignments/alpha_beta_hydrolase_fold.aln.faa
data/classifier/msa/alignments/aspS.aln.faa
data/classifier/msa/alignments/atpG.aln.faa
data/classifier/msa/alignments/ccmC.aln.faa
data/classifier/msa/alignments/ccmE.aln.faa
data/classifier/msa/alignments/cell_division_trigger_factor.aln.faa
data/classifier/msa/alignments/coaD.aln.faa
data/classifier/msa/alignments/coaE.aln.faa
data/classifier/msa/alignments/copper_homeostasis.aln.faa
data/classifier/msa/alignments/cytidylate_kinase.aln.faa
data/classifier/msa/alignments/cytochrome_oxidase_assembly.aln.faa
data/classifier/msa/alignments/dapD.aln.faa
data/classifier/msa/alignments/delta_AAD.aln.faa
data/classifier/msa/alignments/dnaA_1.aln.faa
data/classifier/msa/alignments/dut_deoxyuridine_TN.aln.faa
data/classifier/msa/alignments/eno_hydratase.aln.faa
data/classifier/msa/alignments/exonuclease.aln.faa
data/classifier/msa/alignments/fabZ.aln.faa
data/classifier/msa/alignments/folylpolyglutamate_synth.aln.faa
data/classifier/msa/alignments/fpg.aln.faa
data/classifier/msa/alignments/frr.aln.faa
data/classifier/msa/alignments/gatB.aln.faa
data/classifier/msa/alignments/gidA.aln.faa
data/classifier/msa/alignments/gidB.aln.faa
data/classifier/msa/alignments/glyS.aln.faa
data/classifier/msa/alignments/gpsA.aln.faa
data/classifier/msa/alignments/grla.aln.faa
data/classifier/msa/alignments/grxC.aln.faa
data/classifier/msa/alignments/hemE.aln.faa
data/classifier/msa/alignments/heme_chaperone.aln.faa
data/classifier/msa/alignments/hydrolase_TatD_family.aln.faa
data/classifier/msa/alignments/hypothetical_protein_01.aln.faa
data/classifier/msa/alignments/hypothetical_protein_02.aln.faa
data/classifier/msa/alignments/hypothetical_protein_03.aln.faa
data/classifier/msa/alignments/hypothetical_protein_04.aln.faa
data/classifier/msa/alignments/hypothetical_protein_05.aln.faa
data/classifier/msa/alignments/hypothetical_protein_06.aln.faa
data/classifier/msa/alignments/hypothetical_protein_07.aln.faa
data/classifier/msa/alignments/hypothetical_protein_08.aln.faa
data/classifier/msa/alignments/hypothetical_protein_09.aln.faa
data/classifier/msa/alignments/hypothetical_protein_12.aln.faa
data/classifier/msa/alignments/hypothetical_protein_14.aln.faa
data/classifier/msa/alignments/infC.aln.faa
data/classifier/msa/alignments/iojap_protein_family.aln.faa
data/classifier/msa/alignments/ksgA.aln.faa
data/classifier/msa/alignments/lipoate_protein_ligase_B.aln.faa
data/classifier/msa/alignments/lipoyl_synthase.aln.faa
data/classifier/msa/alignments/maf.aln.faa
data/classifier/msa/alignments/malate_dehydrogenase.aln.faa
data/classifier/msa/alignments/mesJ.aln.faa
data/classifier/msa/alignments/metallo_beta_lactamase.aln.faa
data/classifier/msa/alignments/methylase.aln.faa
data/classifier/msa/alignments/miaA.aln.faa
data/classifier/msa/alignments/mnmA.aln.faa
data/classifier/msa/alignments/murF.aln.faa
data/classifier/msa/alignments/murG.aln.faa
data/classifier/msa/alignments/nifR3_TIM.aln.faa
data/classifier/msa/alignments/nucleoside_diphosphate_kinase.aln.faa
data/classifier/msa/alignments/nuoJ.aln.faa
data/classifier/msa/alignments/nuoK2.aln.faa
data/classifier/msa/alignments/nusA.aln.faa
data/classifier/msa/alignments/nusG.aln.faa
data/classifier/msa/alignments/parvulin_like_PPI.aln.faa
data/classifier/msa/alignments/peptidyl_tRNA_hydrolase.aln.faa
data/classifier/msa/alignments/pgk_phosphoglycerate_kinase.aln.faa
data/classifier/msa/alignments/pgsA.aln.faa
data/classifier/msa/alignments/phage_SPO1_related.aln.faa
data/classifier/msa/alignments/pheT.aln.faa
data/classifier/msa/alignments/phospho_N_APT.aln.faa
data/classifier/msa/alignments/plsX.aln.faa
data/classifier/msa/alignments/polyA_polymerase.aln.faa
data/classifier/msa/alignments/porphobilinogen_deaminase.aln.faa
data/classifier/msa/alignments/protein_S6.aln.faa
data/classifier/msa/alignments/putative_DNA_binding.aln.faa
data/classifier/msa/alignments/putative_zinc_metallo.aln.faa
data/classifier/msa/alignments/pyrG.aln.faa
data/classifier/msa/alignments/quinone_oxi.aln.faa
data/classifier/msa/alignments/rRNA_LS_methyltransferase.aln.faa
data/classifier/msa/alignments/recA.aln.faa
data/classifier/msa/alignments/recombination_protein_RecR.aln.faa
data/classifier/msa/alignments/ribonuclease_E.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L1.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L11.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L13.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L14.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L15.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L17.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L18.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L19.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L2.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L21.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L22.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L23.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L24.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L27.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L28.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L3.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L4.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L5.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L6.aln.faa
data/classifier/msa/alignments/ribosomal_protein_L9.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S10.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S11.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S12.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S13.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S14.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S15.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S16.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S17.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S18.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S19.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S2.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S20.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S3.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S4.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S5.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S7.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S8.aln.faa
data/classifier/msa/alignments/ribosomal_protein_S9.aln.faa
data/classifier/msa/alignments/rnhB.aln.faa
data/classifier/msa/alignments/rplT.aln.faa
data/classifier/msa/alignments/rrm1.aln.faa
data/classifier/msa/alignments/sdhC_556_sub.aln.faa
data/classifier/msa/alignments/secY.aln.faa
data/classifier/msa/alignments/serS.aln.faa
data/classifier/msa/alignments/smpB.aln.faa
data/classifier/msa/alignments/sucA.aln.faa
data/classifier/msa/alignments/tRNA_guanine_N7_MT.aln.faa
data/classifier/msa/alignments/tatc.aln.faa
data/classifier/msa/alignments/tetrapyrrole_methylase.aln.faa
data/classifier/msa/alignments/tgt.aln.faa
data/classifier/msa/alignments/tmk.aln.faa
data/classifier/msa/alignments/tolB.aln.faa
data/classifier/msa/alignments/transcriptional_regulator.aln.faa
data/classifier/msa/alignments/trmD.aln.faa
data/classifier/msa/alignments/trmE.aln.faa
data/classifier/msa/alignments/truA.aln.faa
data/classifier/msa/alignments/tryptophanyl_tRNA_synth.aln.faa
data/classifier/msa/alignments/ubiA.aln.faa
data/classifier/msa/alignments/ubiE.aln.faa
data/classifier/msa/alignments/uvrC.aln.faa
data/mapper/og_metadata.tsv
data/mapper/og_thresholds.tsv
src/sar11_genome_atlas_tools.egg-info/PKG-INFO
src/sar11_genome_atlas_tools.egg-info/SOURCES.txt
src/sar11_genome_atlas_tools.egg-info/dependency_links.txt
src/sar11_genome_atlas_tools.egg-info/entry_points.txt
src/sar11_genome_atlas_tools.egg-info/requires.txt
src/sar11_genome_atlas_tools.egg-info/top_level.txt
src/sga_toolkit/__init__.py
src/sga_toolkit/config.py
src/sga_toolkit/db.py
src/sga_toolkit/exceptions.py
src/sga_toolkit/provenance.py
src/sga_toolkit/runner.py
src/sga_toolkit/ui.py
src/sga_toolkit/classifier/__init__.py
src/sga_toolkit/classifier/alignment.py
src/sga_toolkit/classifier/ani.py
src/sga_toolkit/classifier/classify.py
src/sga_toolkit/classifier/markers.py
src/sga_toolkit/classifier/placement.py
src/sga_toolkit/classifier/taxonomy.py
src/sga_toolkit/cli/__init__.py
src/sga_toolkit/cli/classify.py
src/sga_toolkit/cli/db.py
src/sga_toolkit/cli/map.py
src/sga_toolkit/cli/run.py
src/sga_toolkit/io/__init__.py
src/sga_toolkit/io/fasta.py
src/sga_toolkit/io/inputs.py
src/sga_toolkit/io/jplace.py
src/sga_toolkit/io/tsv.py
src/sga_toolkit/mapper/__init__.py
src/sga_toolkit/mapper/annotate.py
src/sga_toolkit/mapper/hits.py
src/sga_toolkit/mapper/metadata.py