README.md
setup.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/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/dark-matter-version.py
bin/describe-protein-database.py
bin/dna-to-aa.py
bin/download-genbank.sh
bin/e-value-to-bit-score.py
bin/extract-ORFs.py
bin/fasta-base-indices.py
bin/fasta-count.py
bin/fasta-diff.sh
bin/fasta-identity-table.py
bin/fasta-ids.py
bin/fasta-join.py
bin/fasta-lengths.py
bin/fasta-sequences.py
bin/fasta-sort.py
bin/fasta-split-by-id.py
bin/fasta-subset.py
bin/fasta-subtraction.py
bin/fasta-to-phylip.py
bin/fasta-variable-sites.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/find-hits.py
bin/format-fasta.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/local-align.py
bin/make-consensus.py
bin/make-fasta-database.py
bin/make-protein-database.py
bin/ncbi-fetch-id.py
bin/newick-to-ascii.py
bin/noninteractive-alignment-panel.py
bin/parse-genbank-flat-file.py
bin/position-summary.py
bin/pre-commit.sh
bin/print-blast-xml-for-derek.py
bin/print-blast-xml.py
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/relabel-newick-tree.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/split-fasta-by-adaptors.py
bin/subset-protein-database.py
bin/summarize-fasta-bases.py
bin/summarize-reads.py
bin/trim-primers.py
bin/trim-reads.py
bin/write-htcondor-job-spec.py
dark/__init__.py
dark/aa.py
dark/aligners.py
dark/alignments.py
dark/analyze_reads.py
dark/baseimage.py
dark/bowtie2.py
dark/btop.py
dark/cigar.py
dark/codonDistance.py
dark/colors.py
dark/consensus.py
dark/database.py
dark/dimension.py
dark/distance.py
dark/dna.py
dark/entrez.py
dark/errors.py
dark/fasta.py
dark/fasta_ss.py
dark/fastq.py
dark/features.py
dark/filter.py
dark/fpcache.py
dark/genbank.py
dark/genomes.py
dark/graphics.py
dark/hsp.py
dark/html.py
dark/intervals.py
dark/ipynb.py
dark/local_align.py
dark/mutations.py
dark/ncbidb.py
dark/orfs.py
dark/process.py
dark/proteins.py
dark/reads.py
dark/sam.py
dark/score.py
dark/sequence.py
dark/simplify.py
dark/summarize.py
dark/taxonomy.py
dark/titles.py
dark/utils.py
dark/blast/__init__.py
dark/blast/alignments.py
dark/blast/conversion.py
dark/blast/hacks.py
dark/blast/hsp.py
dark/blast/params.py
dark/blast/records.py
dark/blast/score.py
dark/civ/__init__.py
dark/civ/graphics.py
dark/civ/html.py
dark/civ/proteins.py
dark/diamond/__init__.py
dark/diamond/alignments.py
dark/diamond/conversion.py
dark/diamond/hsp.py
dark/diamond/run.py
dark/diamond/sam.py
dark_matter.egg-info/PKG-INFO
dark_matter.egg-info/SOURCES.txt
dark_matter.egg-info/dependency_links.txt
dark_matter.egg-info/pbr.json
dark_matter.egg-info/requires.txt
dark_matter.egg-info/top_level.txt
test/test_aa.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_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_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_utils.py