CHANGELOG.md
COPYING
MANIFEST.in
README.md
VERSION
requirements.txt
setup.py
Oligotyping/__init__.py
Oligotyping/lib/__init__.py
Oligotyping/lib/b6lib.py
Oligotyping/lib/decomposer.py
Oligotyping/lib/entropy.py
Oligotyping/lib/fastalib.py
Oligotyping/lib/oligotyping.py
Oligotyping/lib/shared.py
Oligotyping/lib/topology.py
Oligotyping/utils/__init__.py
Oligotyping/utils/aligner.py
Oligotyping/utils/blast.py
Oligotyping/utils/constants.py
Oligotyping/utils/cosine_similarity.py
Oligotyping/utils/parsers.py
Oligotyping/utils/random_colors.py
Oligotyping/utils/utils.py
Oligotyping/utils/html/__init__.py
Oligotyping/utils/html/error.py
Oligotyping/utils/html/for_decomposition.py
Oligotyping/utils/html/for_oligotyping.py
Oligotyping/utils/html/scripts/README
Oligotyping/utils/html/scripts/g.pie.js
Oligotyping/utils/html/scripts/g.raphael.js
Oligotyping/utils/html/scripts/jquery-1.7.1.js
Oligotyping/utils/html/scripts/morris.LICENSE
Oligotyping/utils/html/scripts/morris.js
Oligotyping/utils/html/scripts/popup.js
Oligotyping/utils/html/scripts/raphael.LICENSE
Oligotyping/utils/html/scripts/raphael.js
Oligotyping/utils/html/static/colorbar.png
Oligotyping/utils/html/static/header_1.png
Oligotyping/utils/html/static/header_2.png
Oligotyping/utils/html/static/missing_image.png
Oligotyping/utils/html/static/style.css
Oligotyping/utils/html/templates/index_for_decomposition.tmpl
Oligotyping/utils/html/templates/index_for_oligo.tmpl
Oligotyping/utils/html/templates/pie_charts_js.tmpl
Oligotyping/utils/html/templates/single_oligo.tmpl
Oligotyping/visualization/__init__.py
Oligotyping/visualization/decomposition_topology.py
Oligotyping/visualization/entropy_distribution_bar.py
Oligotyping/visualization/frequency_curve_and_entropy.py
Oligotyping/visualization/oligotype_distribution_across_samples.py
Oligotyping/visualization/oligotype_distribution_stack_bar.py
Oligotyping/visualization/oligotype_sets_distribution.py
Unittests/_blast.py
Unittests/_decomposition.py
Unittests/_decomposition_threaded.py
Unittests/_entropy.py
Unittests/_oligotyping.py
Unittests/_utils.py
Unittests/_weightedEntropy.py
Unittests/unittests.py
Unittests/files/500-V6V4-Pelagibacter-WEIGHTED-ENTROPY
Unittests/files/500-V6V4-Pelagibacter-run-test
Unittests/files/500-V6V4-Pelagibacter.fasta
Unittests/files/500-V6V4-Pelagibacter.qual
Unittests/files/clone43-v6v4-environment.txt
Unittests/files/clone43-v6v4-matrix-percent.txt
Unittests/files/clone43-v6v4.fa
Unittests/files/reads-noisy-environment.txt
Unittests/files/reads-noisy-matrix-percent.txt
Unittests/files/reads-noisy.fa
Unittests/files/run_decompose
Unittests/files/unaligned-25K-illumina-ENVIRONMENT.txt
Unittests/files/unaligned-25K-illumina-MATRIX-COUNT.txt
Unittests/files/unaligned-25K-illumina-MATRIX-PERCENT.txt
Unittests/files/unaligned-25K-illumina-OLIGOS-ACROSS-DATASETS-MAX-NORM.txt
Unittests/files/unaligned-25K-illumina-OLIGOS-ACROSS-DATASETS-SUM-NORM.txt
Unittests/files/unaligned-25K-illumina-OLIGOTYPE-SETS.txt
Unittests/files/unaligned-25K-illumina-result.b6
Unittests/files/unaligned-25K-illumina-target.db
Unittests/files/unaligned-25K-illumina-test-entropy.txt
Unittests/files/unaligned-25K-illumina-test-entropy.txt.png
Unittests/files/unaligned-25K-illumina-test.fa
Unittests/files/unaligned-unique-25K-illumina-test.fa
Unittests/files/mock/README
Unittests/files/mock/mapping.txt
Unittests/files/mock/mock-env-aligned.fasta
Unittests/files/mock/mock-env.fasta
bin/decompose
bin/entropy-analysis
bin/o-bars-for-each-column.R
bin/o-boxplots.R
bin/o-cluster-analysis.R
bin/o-create-GG-alignment-template-from-taxon
bin/o-fasta-length-distribution
bin/o-gen-dicts-for-qual-stats
bin/o-gen-stackbar-with-sets-from-ENVIRONMENT
bin/o-generate-consensus-from-alignment
bin/o-generate-environment-from-matrix-counts
bin/o-generate-exclusive-figures
bin/o-generate-gephi-network-file
bin/o-generate-html-output
bin/o-generate-matching-qual-file
bin/o-generate-matrix-files-from-ENVIRONMENT
bin/o-generate-oligo-base-networks
bin/o-get-reads-from-fasta
bin/o-get-sample-info-from-fasta
bin/o-heatmap.R
bin/o-keep-or-remove-samples-from-fasta
bin/o-lines-for-each-column.R
bin/o-metaMDS-analysis-with-metadata.R
bin/o-metaMDS-analysis.R
bin/o-pad-with-gaps
bin/o-populate-datasets-from-VAMPS-download
bin/o-remove-gaps
bin/o-sequence-distances
bin/o-smart-trim
bin/o-stackbar.R
bin/o-subsample-fasta-file
bin/o-subsample-matrix-file
bin/o-treat-homopolymer-regions
bin/o-trim
bin/o-trim-uninformative-columns-from-alignment
bin/o-visualize-distance-matrix.R
bin/o-visualize-qual-scores-along-columns.py
bin/oligotype
oligotyping.egg-info/PKG-INFO
oligotyping.egg-info/SOURCES.txt
oligotyping.egg-info/dependency_links.txt
oligotyping.egg-info/requires.txt
oligotyping.egg-info/top_level.txt