LICENSE.txt
MANIFEST.in
README
README.md
demo.cfg
example.cfg
setup.cfg
setup.py
docs/manual.aux
docs/manual.log
docs/manual.out
docs/manual.pdf
docs/manual.tex
docs/manual.toc
mitre/__init__.py
mitre/command_line.py
mitre/efficient_likelihoods.c
mitre/efficient_likelihoods.pyx
mitre/key_comparison.py
mitre/lambda_quick_test.py
mitre/logit_rule_test.py
mitre/logit_rules.py
mitre/logit_test.py
mitre/main.py
mitre/mcmc_diagnostics.py
mitre/mvnpdf_cholesky.py
mitre/posterior.py
mitre/prior_by_primitive.py
mitre/quick_test.cfg
mitre/rules.py
mitre/simulated_data.py
mitre/template.html
mitre/test.py
mitre/visualization.py
mitre.egg-info/PKG-INFO
mitre.egg-info/SOURCES.txt
mitre.egg-info/dependency_links.txt
mitre.egg-info/entry_points.txt
mitre.egg-info/not-zip-safe
mitre.egg-info/requires.txt
mitre.egg-info/top_level.txt
mitre/comparison_methods/__init__.py
mitre/comparison_methods/sklearn_wrappers.py
mitre/data_processing/__init__.py
mitre/data_processing/crossvalidation.py
mitre/data_processing/data_processing.py
mitre/data_processing/filtering.py
mitre/data_processing/sequencing.py
mitre/data_processing/synthetic_data.py
mitre/data_processing/transforms.py
mitre/example_data/CITATIONS.txt
mitre/example_data/example_settings.cfg
mitre/example_data/bokulich/NOTE
mitre/example_data/bokulich/abundance.csv
mitre/example_data/bokulich/dada2_placements.csv
mitre/example_data/bokulich/placement.jplace
mitre/example_data/bokulich/sample_metadata.csv
mitre/example_data/bokulich/sample_metadata_no_repeats.csv
mitre/example_data/bokulich/seq_info.csv
mitre/example_data/bokulich/sequence_key.fa
mitre/example_data/bokulich/subject_data.csv
mitre/example_data/bokulich/taxaTable.csv
mitre/example_data/david/abundance.csv
mitre/example_data/david/david_long.cfg.lsf
mitre/example_data/david/mothur_placements.csv
mitre/example_data/david/placements.jplace
mitre/example_data/david/sample_metadata.csv
mitre/example_data/david/seq_info.csv
mitre/example_data/david/sequence_key.fa
mitre/example_data/david/subject_data.csv
mitre/example_data/david/taxaTable.csv
mitre/example_data/digiulio/abundance.csv
mitre/example_data/digiulio/dada2_placements.csv
mitre/example_data/digiulio/placement.jplace
mitre/example_data/digiulio/sample_metadata.csv
mitre/example_data/digiulio/seq_info.csv
mitre/example_data/digiulio/sequence_key.fa
mitre/example_data/digiulio/subject_data.csv
mitre/example_data/digiulio/taxaTable.csv
mitre/example_data/digiulio/test.cfg.lsf
mitre/example_data/karelia/README
mitre/example_data/karelia/abundance.csv
mitre/example_data/karelia/add_any_allergy_variables.py
mitre/example_data/karelia/dada2_placements.csv
mitre/example_data/karelia/placement.jplace
mitre/example_data/karelia/sample_data.csv
mitre/example_data/karelia/sample_metadata.csv
mitre/example_data/karelia/seq_info.csv
mitre/example_data/karelia/sequence_key.fa
mitre/example_data/karelia/subject_data.csv
mitre/example_data/karelia/subject_data_augmented.csv
mitre/example_data/karelia/taxaTable.csv
mitre/example_data/t1d/diabimmune_t1d_metaphlan_table.txt
mitre/example_data/t1d/diabimmune_t1d_wgs_metadata.csv
mitre/example_data/t1d/process_t1d_wgs.py
mitre/example_data/t1d/t1d_sample_metadata.csv
mitre/example_data/t1d/t1d_wgs_subject_data.csv
mitre/load_data/__init__.py
mitre/load_data/basic.py
mitre/load_data/distance_based.py
mitre/load_data/pplacer.py
mitre/load_data/taxonomy_annotation.py
mitre/trees/__init__.py
mitre/trees/priors.py
mitre/trees/simulators.py
mitre/trees/utilities.py