LICENSE.txt
MANIFEST.in
README.rst
setup.cfg
setup.py
docs/Makefile
docs/change-backend.sh
docs/create-apidoc.sh
docs/download-tutorial-data.sh
docs/make.bat
docs/venv-docs.sh
docs/source/FreeMono.ttf
docs/source/changes.rst
docs/source/conf.py
docs/source/gff.rst
docs/source/index.rst
docs/source/install.rst
docs/source/introduction.rst
docs/source/library.rst
docs/source/api/mgkit.align.rst
docs/source/api/mgkit.consts.rst
docs/source/api/mgkit.counts.func.rst
docs/source/api/mgkit.counts.glm.rst
docs/source/api/mgkit.counts.rst
docs/source/api/mgkit.counts.scaling.rst
docs/source/api/mgkit.db.dbm.rst
docs/source/api/mgkit.db.mongo.rst
docs/source/api/mgkit.db.rst
docs/source/api/mgkit.filter.common.rst
docs/source/api/mgkit.filter.gff.rst
docs/source/api/mgkit.filter.lists.rst
docs/source/api/mgkit.filter.reads.rst
docs/source/api/mgkit.filter.rst
docs/source/api/mgkit.filter.taxon.rst
docs/source/api/mgkit.graphs.rst
docs/source/api/mgkit.io.blast.rst
docs/source/api/mgkit.io.fasta.rst
docs/source/api/mgkit.io.fastq.rst
docs/source/api/mgkit.io.gff.rst
docs/source/api/mgkit.io.glimmer.rst
docs/source/api/mgkit.io.rst
docs/source/api/mgkit.io.snpdat.rst
docs/source/api/mgkit.io.uniprot.rst
docs/source/api/mgkit.io.utils.rst
docs/source/api/mgkit.kegg.rst
docs/source/api/mgkit.logger.rst
docs/source/api/mgkit.mappings.cazy.rst
docs/source/api/mgkit.mappings.eggnog.rst
docs/source/api/mgkit.mappings.enzyme.rst
docs/source/api/mgkit.mappings.go.rst
docs/source/api/mgkit.mappings.pandas_map.rst
docs/source/api/mgkit.mappings.rst
docs/source/api/mgkit.mappings.taxon.rst
docs/source/api/mgkit.mappings.utils.rst
docs/source/api/mgkit.net.embl.rst
docs/source/api/mgkit.net.pfam.rst
docs/source/api/mgkit.net.rst
docs/source/api/mgkit.net.uniprot.rst
docs/source/api/mgkit.net.utils.rst
docs/source/api/mgkit.plots.abund.rst
docs/source/api/mgkit.plots.boxplot.rst
docs/source/api/mgkit.plots.colors.rst
docs/source/api/mgkit.plots.heatmap.rst
docs/source/api/mgkit.plots.rst
docs/source/api/mgkit.plots.unused.rst
docs/source/api/mgkit.plots.utils.rst
docs/source/api/mgkit.rst
docs/source/api/mgkit.simple_cache.rst
docs/source/api/mgkit.snps.classes.rst
docs/source/api/mgkit.snps.conv_func.rst
docs/source/api/mgkit.snps.filter.rst
docs/source/api/mgkit.snps.funcs.rst
docs/source/api/mgkit.snps.mapper.rst
docs/source/api/mgkit.snps.rst
docs/source/api/mgkit.taxon.rst
docs/source/api/mgkit.utils.common.rst
docs/source/api/mgkit.utils.dictionary.rst
docs/source/api/mgkit.utils.rst
docs/source/api/mgkit.utils.sequence.rst
docs/source/api/mgkit.utils.trans_tables.rst
docs/source/api/mgkit.workflow.add_gff_info.rst
docs/source/api/mgkit.workflow.blast2gff.rst
docs/source/api/mgkit.workflow.extract_gff_info.rst
docs/source/api/mgkit.workflow.fasta_utils.rst
docs/source/api/mgkit.workflow.fastq_utils.rst
docs/source/api/mgkit.workflow.filter_gff.rst
docs/source/api/mgkit.workflow.hmmer2gff.rst
docs/source/api/mgkit.workflow.json2gff.rst
docs/source/api/mgkit.workflow.rst
docs/source/api/mgkit.workflow.sampling_utils.rst
docs/source/api/mgkit.workflow.snp_parser.rst
docs/source/api/mgkit.workflow.taxon_utils.rst
docs/source/api/mgkit.workflow.utils.rst
docs/source/api/modules.rst
docs/source/examples/index.rst
docs/source/examples/tutorial-blast.sh
docs/source/examples/db/example-annotation-db-package.ipynb
docs/source/examples/plots/abund.ipynb
docs/source/examples/plots/boxplot.ipynb
docs/source/examples/plots/heatmap.ipynb
docs/source/examples/plots/misc-plots.ipynb
docs/source/extra/Dockerfile
docs/source/images/lca-tablet.png
docs/source/images/uniprot_taxonomy-figure.png
docs/source/pipeline/Exploring-Metagenomic-Data.ipynb
docs/source/pipeline/blast-pred.rst
docs/source/pipeline/blast2lca.rst
docs/source/pipeline/gene_prediction.rst
docs/source/pipeline/index.rst
docs/source/pipeline/tutorial.rst
docs/source/pipeline/diagrams/count-data-analysis.blockdiag.txt
docs/source/pipeline/diagrams/diversity-analysis.blockdiag.txt
docs/source/pipeline/diagrams/gene_prediction-flowchart-general.blockdiag.txt
docs/source/pipeline/diagrams/quantification.blockdiag.txt
docs/source/pipeline/diagrams/snp_parser.blockdiag.txt
docs/source/scripts/add-gff-info.rst
docs/source/scripts/blast2gff.rst
docs/source/scripts/download-taxonomy.rst
docs/source/scripts/edit_gff.rst
docs/source/scripts/fasta-utils.rst
docs/source/scripts/fastq-utils.rst
docs/source/scripts/filter-gff.rst
docs/source/scripts/get-gff-info.rst
docs/source/scripts/hmmer2gff.rst
docs/source/scripts/index.rst
docs/source/scripts/json2gff.rst
docs/source/scripts/pnps_gen.rst
docs/source/scripts/sampling-utils.rst
docs/source/scripts/snp_analysis.rst
docs/source/scripts/taxon_utils.rst
mgkit/__init__.py
mgkit/align.py
mgkit/consts.py
mgkit/graphs.py
mgkit/kegg.py
mgkit/logger.py
mgkit/simple_cache.py
mgkit/taxon.py
mgkit.egg-info/PKG-INFO
mgkit.egg-info/SOURCES.txt
mgkit.egg-info/dependency_links.txt
mgkit.egg-info/entry_points.txt
mgkit.egg-info/requires.txt
mgkit.egg-info/top_level.txt
mgkit/counts/__init__.py
mgkit/counts/func.py
mgkit/counts/glm.py
mgkit/counts/scaling.py
mgkit/db/__init__.py
mgkit/db/dbm.py
mgkit/db/mongo.py
mgkit/filter/__init__.py
mgkit/filter/common.py
mgkit/filter/gff.py
mgkit/filter/lists.py
mgkit/filter/reads.py
mgkit/filter/taxon.py
mgkit/io/__init__.py
mgkit/io/blast.py
mgkit/io/fasta.py
mgkit/io/fastq.py
mgkit/io/gff.py
mgkit/io/glimmer.py
mgkit/io/snpdat.py
mgkit/io/uniprot.py
mgkit/io/utils.py
mgkit/mappings/__init__.py
mgkit/mappings/cazy.py
mgkit/mappings/eggnog.py
mgkit/mappings/enzyme.py
mgkit/mappings/go.py
mgkit/mappings/pandas_map.py
mgkit/mappings/taxon.py
mgkit/mappings/utils.py
mgkit/net/__init__.py
mgkit/net/embl.py
mgkit/net/pfam.py
mgkit/net/uniprot.py
mgkit/net/utils.py
mgkit/plots/__init__.py
mgkit/plots/abund.py
mgkit/plots/boxplot.py
mgkit/plots/colors.py
mgkit/plots/heatmap.py
mgkit/plots/unused.py
mgkit/plots/utils.py
mgkit/snps/__init__.py
mgkit/snps/classes.py
mgkit/snps/conv_func.py
mgkit/snps/filter.py
mgkit/snps/funcs.py
mgkit/snps/mapper.py
mgkit/utils/__init__.py
mgkit/utils/_sequence.c
mgkit/utils/common.py
mgkit/utils/dictionary.py
mgkit/utils/sequence.py
mgkit/utils/trans_tables.py
mgkit/workflow/__init__.py
mgkit/workflow/add_gff_info.py
mgkit/workflow/blast2gff.py
mgkit/workflow/edit_gff.py
mgkit/workflow/extract_gff_info.py
mgkit/workflow/fasta_utils.py
mgkit/workflow/fastq_utils.py
mgkit/workflow/filter_gff.py
mgkit/workflow/hmmer2gff.py
mgkit/workflow/json2gff.py
mgkit/workflow/pnps_gen.py
mgkit/workflow/sampling_utils.py
mgkit/workflow/snp_parser.py
mgkit/workflow/taxon_utils.py
mgkit/workflow/utils.py
scripts/download-ncbi-taxa.sh
scripts/download-taxonomy.sh
scripts/download-uniprot-taxa.sh
scripts/sort-gff.sh
tests/conftest.py
tests/test_counts_scaling.py
tests/test_db_dbm.py
tests/test_db_mongo.py
tests/test_filter_gff.py
tests/test_filters_snps.py
tests/test_filters_taxon.py
tests/test_init.py
tests/test_io_blast.py
tests/test_io_fasta.py
tests/test_io_fastq.py
tests/test_io_gff.py
tests/test_io_utils.py
tests/test_kegg.py
tests/test_mappings.py
tests/test_mappings_eggnog.py
tests/test_net_pfam.py
tests/test_net_uniprot.py
tests/test_scripts.py
tests/test_snps.py
tests/test_taxon.py
tests/test_utils_common.py
tests/test_utils_dictionary.py
tests/test_utils_sequence.py
tests/data/blast-seq.fa
tests/data/one-seq.fa
tests/data/test-edit.gff
tests/data/test-iter.gff
tests/data/test-seq-aa.fa
tests/data/test-seq-nuc.fa
tests/data/test.gff