python-scripts/README.md
python-scripts/aa-compare.py
python-scripts/aa-info.py
python-scripts/aa-to-dna.py
python-scripts/aa-to-properties.py
python-scripts/adaptor-distances.py
python-scripts/alignment-panel-civ.py
python-scripts/alignments-per-read.py
python-scripts/bit-score-to-e-value.py
python-scripts/bwa-index-to-fasta.py
python-scripts/cat-json-blast-records.py
python-scripts/check-fasta-json-blast-consistency.py
python-scripts/codon-distance.py
python-scripts/combine-sequences.py
python-scripts/compare-aa-sequences.py
python-scripts/compare-consensuses.py
python-scripts/compare-sequences.py
python-scripts/convert-blast-xml-to-json.py
python-scripts/convert-diamond-to-json.py
python-scripts/convert-diamond-to-sam.py
python-scripts/convert-sam-to-fastq.sh
python-scripts/create-newick-relabeling-output.py
python-scripts/curate-tree-ete.py
python-scripts/curate-trees.py
python-scripts/dark-matter-version.py
python-scripts/describe-protein-database.py
python-scripts/dna-to-aa.py
python-scripts/download-genbank.sh
python-scripts/download-refseq-viral-fasta.sh
python-scripts/download-refseq-viral-gbff.sh
python-scripts/e-value-to-bit-score.py
python-scripts/extract-ORFs.py
python-scripts/extract-reference-from-fasta-and-bam.py
python-scripts/extract-reference-from-fasta-and-bam.py~
python-scripts/fasta-base-indices.py
python-scripts/fasta-count-chars.py
python-scripts/fasta-count.py
python-scripts/fasta-coverage.py
python-scripts/fasta-diff.py
python-scripts/fasta-diff.sh
python-scripts/fasta-find.py
python-scripts/fasta-identity-table.py
python-scripts/fasta-ids.py
python-scripts/fasta-join.py
python-scripts/fasta-lengths.py
python-scripts/fasta-match-offsets.py
python-scripts/fasta-sequences.py
python-scripts/fasta-sort.py
python-scripts/fasta-split-by-id.py
python-scripts/fasta-split-by-length.py
python-scripts/fasta-split.py
python-scripts/fasta-subset.py
python-scripts/fasta-subtraction.py
python-scripts/fasta-to-phylip.py
python-scripts/fasta-translate.py
python-scripts/fasta-variable-sites.py
python-scripts/fastq-set-quality.py
python-scripts/filter-fasta-by-complexity.py
python-scripts/filter-fasta-by-taxonomy.py
python-scripts/filter-fasta.py
python-scripts/filter-hits-to-fasta.py
python-scripts/filter-reads-alignments.py
python-scripts/filter-sam.py
python-scripts/format-fasta.py
python-scripts/genbank-grep.py
python-scripts/genome-protein-summary.py
python-scripts/get-features.py
python-scripts/get-hosts.py
python-scripts/get-reads.py
python-scripts/get-taxonomy.py
python-scripts/graph-evalues.py
python-scripts/ids.py
python-scripts/local-align.py
python-scripts/make-consensus.py
python-scripts/make-fasta-database.py
python-scripts/make-protein-database.py
python-scripts/msa-find-and-extract.py
python-scripts/ncbi-fetch-id.py
python-scripts/newick-to-ascii.py
python-scripts/noninteractive-alignment-panel.py
python-scripts/parse-genbank-flat-file.py
python-scripts/plot-coverage-depth.py
python-scripts/plot-references-by-inter-read-distance.py
python-scripts/plot-windowed-identity.py
python-scripts/position-summary.py
python-scripts/pre-commit.sh
python-scripts/print-read-lengths.py
python-scripts/proteins-to-pathogens-civ.py
python-scripts/proteins-to-pathogens.py
python-scripts/randomize-fasta.py
python-scripts/read-blast-json.py
python-scripts/read-blast-xml.py
python-scripts/reference-read-scores-to-JSON.py
python-scripts/relabel-newick-tree.py
python-scripts/remove-alrt-from-tree.py
python-scripts/reverse-complement.py
python-scripts/run-bowtie2.py
python-scripts/run-bwa.py
python-scripts/sam-coverage-depth.py
python-scripts/sam-coverage.py
python-scripts/sam-match-lengths.py
python-scripts/sam-match-lengths.py~
python-scripts/sam-reference-read-counts.py
python-scripts/sam-references.py
python-scripts/sam-to-fasta-alignment.py
python-scripts/sff-to-fastq.py
python-scripts/simple-consensus.py
python-scripts/split-fasta-by-adaptors.py
python-scripts/subset-protein-database.py
python-scripts/summarize-fasta-bases.py
python-scripts/summarize-reads.py
python-scripts/translate.py
python-scripts/tree-info.py
python-scripts/trim-primers.py
python-scripts/trim-reads.py
python-scripts/window-split-alignment.py
python-scripts/write-htcondor-job-spec.py
site-packages/dark/__init__.py
site-packages/dark/aa.py
site-packages/dark/aaVars.py
site-packages/dark/aligners.py
site-packages/dark/alignments.py
site-packages/dark/analyze_reads.py
site-packages/dark/baseimage.py
site-packages/dark/blast/__init__.py
site-packages/dark/blast/alignments.py
site-packages/dark/blast/conversion.py
site-packages/dark/blast/hacks.py
site-packages/dark/blast/hsp.py
site-packages/dark/blast/params.py
site-packages/dark/blast/records.py
site-packages/dark/blast/score.py
site-packages/dark/bowtie2.py
site-packages/dark/btop.py
site-packages/dark/cigar.py
site-packages/dark/civ/__init__.py
site-packages/dark/civ/graphics.py
site-packages/dark/civ/html.py
site-packages/dark/civ/proteins.py
site-packages/dark/codonDistance.py
site-packages/dark/colors.py
site-packages/dark/consensus-with-debugging.py
site-packages/dark/consensus.py
site-packages/dark/database.py
site-packages/dark/diamond/__init__.py
site-packages/dark/diamond/alignments.py
site-packages/dark/diamond/conversion.py
site-packages/dark/diamond/hsp.py
site-packages/dark/diamond/run.py
site-packages/dark/diamond/sam.py
site-packages/dark/dimension.py
site-packages/dark/distance.py
site-packages/dark/dna.py
site-packages/dark/entrez.py
site-packages/dark/errors.py
site-packages/dark/extract_reference.py
site-packages/dark/fasta.py
site-packages/dark/fasta_ss.py
site-packages/dark/fastq.py
site-packages/dark/features.py
site-packages/dark/filter.py
site-packages/dark/fpcache.py
site-packages/dark/genbank.py
site-packages/dark/genomes.py
site-packages/dark/graphics.py
site-packages/dark/hsp.py
site-packages/dark/html.py
site-packages/dark/idutils.py
site-packages/dark/intervals.py
site-packages/dark/ipynb.py
site-packages/dark/local_align.py
site-packages/dark/mutations.py
site-packages/dark/ncbidb.py
site-packages/dark/orfs.py
site-packages/dark/process.py
site-packages/dark/progress.py
site-packages/dark/proteins.py
site-packages/dark/reads.py
site-packages/dark/sam.py
site-packages/dark/score.py
site-packages/dark/sequence.py
site-packages/dark/simplify.py
site-packages/dark/sqlite3.py
site-packages/dark/summarize.py
site-packages/dark/taxonomy.py
site-packages/dark/titles.py
site-packages/dark/trees.py
site-packages/dark/utils.py
site-packages/dark/windowedIdentity.py
site-packages/dark_matter-7.2.0.dist-info/INSTALLER
site-packages/dark_matter-7.2.0.dist-info/METADATA
site-packages/dark_matter-7.2.0.dist-info/RECORD
site-packages/dark_matter-7.2.0.dist-info/REQUESTED
site-packages/dark_matter-7.2.0.dist-info/WHEEL
site-packages/dark_matter-7.2.0.dist-info/direct_url.json
site-packages/dark_matter-7.2.0.dist-info/licenses/LICENSE
site-packages/dark_matter-7.2.0.dist-info/top_level.txt
