.condarc
.gitignore
.gitlab-ci.yml
.pre-commit-config.yaml
CHANGELOG.md
LICENSE
MANIFEST.in
README.MITOS
README.md
SETUP.WWW2
authors.txt
dev_requirements.txt
mypy.ini
pyproject.toml
setup.cfg
tox.ini
eve_scripts/update_hmm_job.sh
mitos/CONFIG.py
mitos/CONFIG.py.sample
mitos/__init__.py
mitos/_version.py
mitos/booreparser.py
mitos/cmsearch_parse_separate.py
mitos/codoncount.py
mitos/convert_tree.py
mitos/create_prot_fasta.py
mitos/get-wancy.py
mitos/inihit.py
mitos/merge_results.py
mitos/mitoch_revisions.py
mitos/mitoloc.py
mitos/mitos-extension.py
mitos/mitos-extension2.py
mitos/mumcmp.py
mitos/names.py
mitos/ogre-geneorder.py
mitos/plot_evalues.R
mitos/plot_gapfractions.R
mitos/plotprot.R
mitos/plotrna.R
mitos/plotstst.R
mitos/prepareFiles.py
mitos/removegene.py
mitos/skew.py
mitos/trna-cm.py
mitos/trnadist.py
mitos/trnascan_parse_separate.py
mitos/update-mitolog.py
mitos.egg-info/PKG-INFO
mitos.egg-info/SOURCES.txt
mitos.egg-info/dependency_links.txt
mitos.egg-info/entry_points.txt
mitos.egg-info/requires.txt
mitos.egg-info/top_level.txt
mitos/bedfile/__init__.py
mitos/blast/__init__.py
mitos/draw/__init__.py
mitos/extprog/__init__.py
mitos/feature/__init__.py
mitos/gb/__init__.py
mitos/gb/unify.py
mitos/gfffile/__init__.py
mitos/mergefeature/__init__.py
mitos/mitfi/__init__.py
mitos/mitfi/parser/improve_infernal_structure.jar
mitos/mitfi/parser/mitfiGeneticCodes
mitos/mitfi/parser/mitfi_import-1.1.jar
mitos/mitfi/parser/mitfi_import-1.1.jar.old
mitos/mitfi/parser/mitfi_import-1.1.jar.org
mitos/mitfi/parser/mitfi_import-1.1.jar.org.pre-circ
mitos/mitfi/parser/mitfi_import.jar
mitos/mito/__init__.py
mitos/mitofile/__init__.py
mitos/protfeat/__init__.py
mitos/rna/__init__.py
mitos/rna/forester.py
mitos/rna/vienna.py
mitos/scripts/__init__.py
mitos/scripts/analyse.py
mitos/scripts/drawmitos.py
mitos/scripts/gcpp.py
mitos/scripts/getfeatures.py
mitos/scripts/getinfo.py
mitos/scripts/refseqsplit.py
mitos/scripts/runmitos.py
mitos/scripts/subseq.py
mitos/scripts/taxtree.py
mitos/scripts/update_blastdb.py
mitos/scripts/update_hmm.py
mitos/sequence/__init__.py
mitos/sequence/degenerate.py
mitos/tax/__init__.py
mitos/tbl/__init__.py
mitos/trna/__init__.py
mitos/trna/arwenscan.py
mitos/trna/trnascan.py
mitos/update/__init__.py
mitos/util/__init__.py
test/MITOS-alphabet.fas
test/MITOS-empty.fas
test/MITOS-multi.fas
test/MITOS-nofasta.fas
test/MITOS-to-large.fas
test/NC_012920.bed
test/NC_012920.fasta
test/NC_019653.gb
test/README
test/dummy_genbank.gb
test/result_NC_012920.mitos
test/result_NC_012920.png
test/result_NC_012920_alarab.mitos
test/result_analyse.txt
test/result_gcpp.txt
test/result_getfeatures.txt
test/result_getinfo.txt
test/result_refseqsplit.gb
test/result_subseq.txt
test/result_taxtree.txt
test/result_update_blastdb.json
test/feature/test_crange.py
test/feature/test_length.py
test/taxtree_test/NC_012920.gb
test/taxtree_test/NC_019653.gb
test/taxtree_test/taxtree_merged.dmp
test/taxtree_test/taxtree_names.dmp
test/taxtree_test/taxtree_nodes.dmp
test/update_blastdb_test/NC_012920.bed
test/update_blastdb_test/NC_012920.gb
test/update_hmm_test/NC_012920.gb
test/update_hmm_test/NC_019653.gb
test/update_hmm_test/cox1.db
test/update_hmm_test/nad2.db
test/update_hmm_test/test_extract_protein_sequences.py
test/update_hmm_test/test_filter_best_per_target.py
test/update_hmm_test/update_hmm_check_output.py
test/update_hmm_test/expected/cox1_expected.db
test/update_hmm_test/expected/nad2_expected.db