LICENSE
README.md
pyproject.toml
bin/README.md
bin/aa-compare.py
bin/aa-info.py
bin/aa-to-dna.py
bin/aa-to-properties.py
bin/adaptor-distances.py
bin/alignment-panel-civ.py
bin/alignments-per-read.py
bin/bit-score-to-e-value.py
bin/cat-json-blast-records.py
bin/check-fasta-json-blast-consistency.py
bin/codon-distance.py
bin/combine-sequences.py
bin/compare-aa-sequences.py
bin/compare-consensuses.py
bin/compare-sequences.py
bin/convert-blast-xml-to-json.py
bin/convert-diamond-to-json.py
bin/convert-diamond-to-sam.py
bin/convert-sam-to-fastq.sh
bin/create-newick-relabeling-output.py
bin/curate-tree-ete.py
bin/curate-trees.py
bin/dark-matter-version.py
bin/describe-protein-database.py
bin/dna-to-aa.py
bin/download-genbank.sh
bin/download-refseq-viral-fasta.sh
bin/download-refseq-viral-gbff.sh
bin/e-value-to-bit-score.py
bin/extract-ORFs.py
bin/extract-reference-from-fasta-and-bam.py
bin/extract-reference-from-fasta-and-bam.py~
bin/fasta-base-indices.py
bin/fasta-count-chars.py
bin/fasta-count.py
bin/fasta-coverage.py
bin/fasta-diff.sh
bin/fasta-find.py
bin/fasta-identity-table.py
bin/fasta-ids.py
bin/fasta-join.py
bin/fasta-lengths.py
bin/fasta-match-offsets.py
bin/fasta-sequences.py
bin/fasta-sort.py
bin/fasta-split-by-id.py
bin/fasta-split-by-length.py
bin/fasta-split.py
bin/fasta-subset.py
bin/fasta-subtraction.py
bin/fasta-to-phylip.py
bin/fasta-translate.py
bin/fasta-variable-sites.py
bin/fastq-set-quality.py
bin/filter-fasta-by-complexity.py
bin/filter-fasta-by-taxonomy.py
bin/filter-fasta.py
bin/filter-hits-to-fasta.py
bin/filter-reads-alignments.py
bin/filter-sam.py
bin/format-fasta.py
bin/genbank-grep.py
bin/genome-protein-summary.py
bin/get-features.py
bin/get-hosts.py
bin/get-reads.py
bin/get-taxonomy.py
bin/graph-evalues.py
bin/ids.py
bin/local-align.py
bin/make-consensus.py
bin/make-fasta-database.py
bin/make-protein-database.py
bin/msa-find-and-extract.py
bin/ncbi-fetch-id.py
bin/newick-to-ascii.py
bin/noninteractive-alignment-panel.py
bin/parse-genbank-flat-file.py
bin/plot-references-by-inter-read-distance.py
bin/plot-windowed-identity.py
bin/position-summary.py
bin/pre-commit.sh
bin/print-read-lengths.py
bin/proteins-to-pathogens-civ.py
bin/proteins-to-pathogens.py
bin/randomize-fasta.py
bin/read-blast-json.py
bin/read-blast-xml.py
bin/reference-read-scores-to-JSON.py
bin/relabel-newick-tree.py
bin/remove-alrt-from-tree.py
bin/reverse-complement.py
bin/run-bowtie2.py
bin/run-bwa.py
bin/sam-coverage-depth.py
bin/sam-coverage.py
bin/sam-reference-read-counts.py
bin/sam-references.py
bin/sam-to-fasta-alignment.py
bin/sff-to-fastq.py
bin/simple-consensus.py
bin/split-fasta-by-adaptors.py
bin/subset-protein-database.py
bin/summarize-fasta-bases.py
bin/summarize-reads.py
bin/translate.py
bin/tree-info.py
bin/trim-primers.py
bin/trim-reads.py
bin/window-split-alignment.py
bin/write-htcondor-job-spec.py
src/dark/__init__.py
src/dark/aa.py
src/dark/aaVars.py
src/dark/aligners.py
src/dark/alignments.py
src/dark/analyze_reads.py
src/dark/baseimage.py
src/dark/bowtie2.py
src/dark/btop.py
src/dark/cigar.py
src/dark/codonDistance.py
src/dark/colors.py
src/dark/consensus-with-debugging.py
src/dark/consensus.py
src/dark/database.py
src/dark/dimension.py
src/dark/distance.py
src/dark/dna.py
src/dark/entrez.py
src/dark/errors.py
src/dark/extract_reference.py
src/dark/fasta.py
src/dark/fasta_ss.py
src/dark/fastq.py
src/dark/features.py
src/dark/filter.py
src/dark/fpcache.py
src/dark/genbank.py
src/dark/genomes.py
src/dark/graphics.py
src/dark/hsp.py
src/dark/html.py
src/dark/idutils.py
src/dark/intervals.py
src/dark/ipynb.py
src/dark/local_align.py
src/dark/mutations.py
src/dark/ncbidb.py
src/dark/orfs.py
src/dark/process.py
src/dark/progress.py
src/dark/proteins.py
src/dark/reads.py
src/dark/sam.py
src/dark/score.py
src/dark/sequence.py
src/dark/simplify.py
src/dark/sqlite3.py
src/dark/summarize.py
src/dark/taxonomy.py
src/dark/titles.py
src/dark/trees.py
src/dark/utils.py
src/dark/windowedIdentity.py
src/dark/blast/__init__.py
src/dark/blast/alignments.py
src/dark/blast/conversion.py
src/dark/blast/hacks.py
src/dark/blast/hsp.py
src/dark/blast/params.py
src/dark/blast/records.py
src/dark/blast/score.py
src/dark/civ/__init__.py
src/dark/civ/graphics.py
src/dark/civ/html.py
src/dark/civ/proteins.py
src/dark/diamond/__init__.py
src/dark/diamond/alignments.py
src/dark/diamond/conversion.py
src/dark/diamond/hsp.py
src/dark/diamond/run.py
src/dark/diamond/sam.py
src/dark_matter.egg-info/PKG-INFO
src/dark_matter.egg-info/SOURCES.txt
src/dark_matter.egg-info/dependency_links.txt
src/dark_matter.egg-info/requires.txt
src/dark_matter.egg-info/top_level.txt
test/test_aa.py
test/test_aligners.py
test/test_alignments.py
test/test_analyze_reads.py
test/test_bowtie2.py
test/test_btop.py
test/test_cigar.py
test/test_codonDistance.py
test/test_colors.py
test/test_consensus.py
test/test_dimension.py
test/test_distance.py
test/test_dna.py
test/test_fasta.py
test/test_fasta_ss.py
test/test_fastq.py
test/test_features.py
test/test_filter.py
test/test_genbank.py
test/test_genomes.py
test/test_graphics.py
test/test_hsp.py
test/test_html.py
test/test_idutils.py
test/test_intervals.py
test/test_local_align.py
test/test_mutations.py
test/test_orfs.py
test/test_process.py
test/test_proteins.py
test/test_reads.py
test/test_sam.py
test/test_score.py
test/test_sequence.py
test/test_simplify.py
test/test_summarize.py
test/test_taxonomy.py
test/test_titles.py
test/test_trees.py
test/test_utils.py
test/test_windowedIdentity.py