LICENCE.txt
MANIFEST.in
README.md
SILVA.LICENCE.txt
setup.py
bin/graftM
graftm/__init__.py
graftm/archive.py
graftm/classify.py
graftm/clusterer.py
graftm/create.py
graftm/db_search_results.py
graftm/decorator.py
graftm/decoy_filter.py
graftm/deduplicator.py
graftm/dendropy_tree_cleaner.py
graftm/diamond.py
graftm/expand_searcher.py
graftm/external_program_suite.py
graftm/getaxnseq.py
graftm/graftm_output_paths.py
graftm/graftm_package.py
graftm/greengenes_taxonomy.py
graftm/hmmsearcher.py
graftm/housekeeping.py
graftm/orfm.py
graftm/pplacer.py
graftm/readHmmTable.py
graftm/reannotator.py
graftm/rerooter.py
graftm/run.py
graftm/search_table.py
graftm/sequence_extractor.py
graftm/sequence_io.py
graftm/sequence_search_results.py
graftm/sequence_searcher.py
graftm/summarise.py
graftm/taxonomy_cleaner.py
graftm/taxonomy_extractor.py
graftm/timeit.py
graftm/tree_decorator.py
graftm/unpack_sequences.py
graftm/update.py
graftm/version.py
graftm.egg-info/PKG-INFO
graftm.egg-info/SOURCES.txt
graftm.egg-info/dependency_links.txt
graftm.egg-info/requires.txt
graftm.egg-info/top_level.txt
share/18S.hmm
test/test_archive.py
test/test_clusterer.py
test/test_create.py
test/test_decoy_filter.py
test/test_deduplicator.py
test/test_dendropy_tree_cleaner.py
test/test_diamond.py
test/test_expand_searcher.py
test/test_external_program_suite.py
test/test_getaxnseq.py
test/test_graft.py
test/test_graftm_package.py
test/test_greengenes_taxonomy.py
test/test_hmmer.py
test/test_hmmsearcher.py
test/test_json_placement_split.py
test/test_reroot.py
test/test_running_utils.py
test/test_sequence_extractor.py
test/test_sequence_search_result.py
test/test_summarise.py
test/test_taxonomy_extractor.py
test/test_unpack_sequences.py
test/test_update.py
test/data/aa_orf_split_bug.fna
test/data/random_paired.fna
test/data/s19.hmm
test/data/16S_inputs/16S_1.1.fa
test/data/16S_inputs/16S_1.2.fa
test/data/16S_inputs/16S_2.1.fa
test/data/16S_inputs/16S_2.2.fa
test/data/61_otus.gpkg/61_otus.hmm
test/data/61_otus.gpkg/CONTENTS.json
test/data/61_otus.gpkg/61_otus.refpkg/61_otus.aln.fa
test/data/61_otus.gpkg/61_otus.refpkg/61_otus.tre
test/data/61_otus.gpkg/61_otus.refpkg/61_otus.tre.log
test/data/61_otus.gpkg/61_otus.refpkg/61_otus_seqinfo.csv
test/data/61_otus.gpkg/61_otus.refpkg/61_otus_taxonomy.csv
test/data/61_otus.gpkg/61_otus.refpkg/CONTENTS.json
test/data/61_otus.gpkg/61_otus.refpkg/phylo_modeluFfo38.json
test/data/61_otus.gpkg/61_otus.refpkg/treeXec3T9.tre
test/data/S1.2.ribosomal_protein_L3_rplC/4.dmnd
test/data/S1.2.ribosomal_protein_L3_rplC/CONTENTS.json
test/data/S1.2.ribosomal_protein_L3_rplC/DNGNGWU00012_mingle_output_good_seqs.hmm
test/data/S1.2.ribosomal_protein_L3_rplC/graftmID8t_I_search.hmm
test/data/S1.2.ribosomal_protein_L3_rplC/graftm_VEYiP.faa
test/data/S1.2.ribosomal_protein_L3_rplC/graftmeZ00Qg_search.hmm
test/data/S1.2.ribosomal_protein_L3_rplC/4.08.ribosomal_protein_L3_rplC_final.gpkg.refpkg/4.tre
test/data/S1.2.ribosomal_protein_L3_rplC/4.08.ribosomal_protein_L3_rplC_final.gpkg.refpkg/4.tre.log
test/data/S1.2.ribosomal_protein_L3_rplC/4.08.ribosomal_protein_L3_rplC_final.gpkg.refpkg/4_deduplicated_aligned.fasta
test/data/S1.2.ribosomal_protein_L3_rplC/4.08.ribosomal_protein_L3_rplC_final.gpkg.refpkg/4_seqinfo.csv
test/data/S1.2.ribosomal_protein_L3_rplC/4.08.ribosomal_protein_L3_rplC_final.gpkg.refpkg/4_taxonomy.csv
test/data/S1.2.ribosomal_protein_L3_rplC/4.08.ribosomal_protein_L3_rplC_final.gpkg.refpkg/CONTENTS.json
test/data/S1.2.ribosomal_protein_L3_rplC/4.08.ribosomal_protein_L3_rplC_final.gpkg.refpkg/phylo_modeltn6nXl.json
test/data/S1.2.ribosomal_protein_L3_rplC/4.08.ribosomal_protein_L3_rplC_final.gpkg.refpkg/treeuMje7j.tre
test/data/bootstrapper/DNGNGWU00001.hmm
test/data/bootstrapper/contigs.fna
test/data/bootstrapper/diamond_bootstrap_contigs.fna
test/data/bootstrapper/diamond_bootstrap_reads.fna
test/data/bootstrapper/expected.hmm
test/data/bootstrapper/D1_gpkg_for_diamond.gpkg/CONTENTS.json
test/data/bootstrapper/D1_gpkg_for_diamond.gpkg/DNGNGWU00001_mingle_output_good_seqs.dmnd
test/data/bootstrapper/D1_gpkg_for_diamond.gpkg/DNGNGWU00001_mingle_output_good_seqs.hmm
test/data/bootstrapper/D1_gpkg_for_diamond.gpkg/DNGNGWU00001_mingle_output_good_seqs.hmm.single_copies.fasta
test/data/bootstrapper/D1_gpkg_for_diamond.gpkg/1.gpkg.refpkg/CONTENTS.json
test/data/bootstrapper/D1_gpkg_for_diamond.gpkg/1.gpkg.refpkg/DNGNGWU00001_mingle_output_good_seqs.tre
test/data/bootstrapper/D1_gpkg_for_diamond.gpkg/1.gpkg.refpkg/DNGNGWU00001_mingle_output_good_seqs.tre.log
test/data/bootstrapper/D1_gpkg_for_diamond.gpkg/1.gpkg.refpkg/DNGNGWU00001_mingle_output_good_seqs_deduplicated_aligned.fasta
test/data/bootstrapper/D1_gpkg_for_diamond.gpkg/1.gpkg.refpkg/DNGNGWU00001_mingle_output_good_seqs_seqinfo.csv
test/data/bootstrapper/D1_gpkg_for_diamond.gpkg/1.gpkg.refpkg/DNGNGWU00001_mingle_output_good_seqs_taxonomy.csv
test/data/bootstrapper/D1_gpkg_for_diamond.gpkg/1.gpkg.refpkg/phylo_modelMEgkVy.json
test/data/bootstrapper/D1_gpkg_for_diamond.gpkg/1.gpkg.refpkg/treeSNpXl4.tre
test/data/create/61_otus.fasta
test/data/create/61_otus.without_4459468.aln.fasta
test/data/create/61_otus.without_4459468.fasta
test/data/create/61_otus.without_4459468.tre
test/data/create/decorated.tree
test/data/create/first5.hmm
test/data/create/homologs.hmm
test/data/create/homologs.tax2tree.rerooted.decorated.tree-consensus-strings
test/data/create/homologs.trimmed.aligned.duplicate.faa
test/data/create/homologs.trimmed.aligned.faa
test/data/create/homologs.trimmed.unaligned.duplicate_seq.faa
test/data/create/homologs.trimmed.unaligned.faa
test/data/create/homologs.trimmed.unaligned.with_stars.faa
test/data/create/homologstre.tree
test/data/create/sulfitereductase.ben.tree
test/data/create/test.faa
test/data/diamond/mcra.faa
test/data/diamond/mcra.faa.dmnd
test/data/hmms/DNGNGWU00027.hmm
test/data/mcrA.10seqs.gpkg/CONTENTS.json
test/data/mcrA.10seqs.gpkg/graftmFWdYLV_align.hmm
test/data/mcrA.10seqs.gpkg/graftmlTzkCs_search.hmm
test/data/mcrA.10seqs.gpkg/mcra10.dmnd
test/data/mcrA.10seqs.gpkg/mcra10.fa
test/data/mcrA.10seqs.gpkg/mcrA.10seqs.gpkg.refpkg/CONTENTS.json
test/data/mcrA.10seqs.gpkg/mcrA.10seqs.gpkg.refpkg/mcrA_seq.csv
test/data/mcrA.10seqs.gpkg/mcrA.10seqs.gpkg.refpkg/mcrA_taxonomy.csv
test/data/mcrA.10seqs.gpkg/mcrA.10seqs.gpkg.refpkg/mcra10.tre
test/data/mcrA.10seqs.gpkg/mcrA.10seqs.gpkg.refpkg/mcra10.tre.log
test/data/mcrA.10seqs.gpkg/mcrA.10seqs.gpkg.refpkg/mcra10_deduplicated_aligned.fasta
test/data/mcrA.10seqs.gpkg/mcrA.10seqs.gpkg.refpkg/phylo_modelytj56R.json
test/data/mcrA.10seqs.gpkg/mcrA.10seqs.gpkg.refpkg/treeoI0eFz.tre
test/data/mcrA.gpkg/CONTENTS.json
test/data/mcrA.gpkg/mcrA.faa
test/data/mcrA.gpkg/mcrA.hmm
test/data/mcrA.gpkg/mcrA_1.1.faa
test/data/mcrA.gpkg/mcrA_1.1.fna
test/data/mcrA.gpkg/mcrA_1.2.faa
test/data/mcrA.gpkg/mcrA_1.2.fna
test/data/mcrA.gpkg/mcrA_2.1.faa
test/data/mcrA.gpkg/mcrA_2.1.fna
test/data/mcrA.gpkg/mcrA_2.2.faa
test/data/mcrA.gpkg/mcrA_2.2.fna
test/data/mcrA.gpkg/mcra.faa.dmnd
test/data/mcrA.gpkg/mcrA.refpkg/CONTENTS.json
test/data/mcrA.gpkg/mcrA.refpkg/mcrA.aln.fasta
test/data/mcrA.gpkg/mcrA.refpkg/mcrA_db2.fasta
test/data/mcrA.gpkg/mcrA.refpkg/mcrA_db2.fasta.tre.log
test/data/mcrA.gpkg/mcrA.refpkg/mcrA_db2.tre
test/data/mcrA.gpkg/mcrA.refpkg/mcrA_seq.csv
test/data/mcrA.gpkg/mcrA.refpkg/mcrA_taxonomy.csv
test/data/mcrA.gpkg/mcrA.refpkg/phylo_modelH1EJOP.json
test/data/mcrA.gpkg/mcrA.refpkg/treeoN87dL.tre
test/data/mcrA_second_half.gpkg/mcrA.300-557.aln.fasta
test/data/mcrA_second_half.gpkg/mcrA.300-557.aln.fasta.hmm
test/data/mcrA_with_dmnd.gpkg/CONTENTS.json
test/data/mcrA_with_dmnd.gpkg/homologs.dmnd
test/data/mcrA_with_dmnd.gpkg/homologs.faa
test/data/mcrA_with_dmnd.gpkg/homologs_0.hmm
test/data/mcrA_with_dmnd.gpkg/homologs.refpkg/CONTENTS.json
test/data/mcrA_with_dmnd.gpkg/homologs.refpkg/graftmMUpy0V.tree
test/data/mcrA_with_dmnd.gpkg/homologs.refpkg/graftmqxMB0b.tree_log
test/data/mcrA_with_dmnd.gpkg/homologs.refpkg/homologs_deduplicated_aligned.fasta
test/data/mcrA_with_dmnd.gpkg/homologs.refpkg/homologs_seqinfo.csv
test/data/mcrA_with_dmnd.gpkg/homologs.refpkg/homologs_taxonomy.csv
test/data/mcrA_with_dmnd.gpkg/homologs.refpkg/phylo_model9eDX4K.json
test/sample_runs/sample_16S_1.1.fa
test/sample_runs/sample_16S_1.2.fa
test/sample_runs/sample_16S_2.1.fa
test/sample_runs/sample_16S_2.2.fa
test/sample_runs/sample_mcrA_1.1.fa
test/sample_runs/sample_mcrA_1.2.fa
test/sample_runs/sample_mcrA_2.1.fa
test/sample_runs/sample_mcrA_2.2.fa