├── .coveragerc ├── .gitignore ├── .travis.yml ├── LICENSE ├── README.rst ├── ghosttree ├── __init__.py ├── extensions │ ├── __init__.py │ └── cluster.py ├── filter.py ├── scaffold │ ├── __init__.py │ ├── hybridtree.py │ └── tests │ │ ├── __init__.py │ │ └── test_hybridtree.py ├── silva │ ├── __init__.py │ ├── filter.py │ └── tests │ │ ├── __init__.py │ │ └── test_filter.py ├── tests │ ├── __init__.py │ ├── test_filter.py │ └── test_util.py └── util.py ├── helper_files └── get_otus_from_ghost_tree.py ├── licenses └── scikit-bio.txt ├── scripts └── ghost-tree ├── setup.cfg ├── setup.py ├── trees ├── README.rst ├── tree_archive │ ├── README.rst │ ├── ghost-trees_052515 │ │ ├── ghosttree_UNITEv6_10.09.2014_97_100_052515.nwk │ │ ├── ghosttree_UNITEv6_10.09.2014_97_80_052515.nwk │ │ ├── ghosttree_UNITEv6_10.09.2014_99_100_052515.nwk │ │ ├── ghosttree_UNITEv6_10.09.2014_99_80_052515.nwk │ │ ├── ghosttree_UNITEv6_10.09.2014_dynamic_100_052515.nwk │ │ ├── ghosttree_UNITEv6_10.09.2014_dynamic_80_052515.nwk │ │ ├── ghosttree_UNITEv6_30.12.2014S_97_100clusters_052515.nwk │ │ ├── ghosttree_UNITEv6_30.12.2014S_97_80clusters_052515.nwk │ │ ├── ghosttree_UNITEv6_30.12.2014S_99_100clusters_052515.nwk │ │ ├── ghosttree_UNITEv6_30.12.2014S_99_80clusters_052515.nwk │ │ ├── ghosttree_UNITEv6_30.12.2014S_dynamic_100clusters_052515.nwk │ │ ├── ghosttree_UNITEv6_30.12.2014S_dynamic_80clusters_052515.nwk │ │ ├── ghosttree_UNITEv6_30.12.2014_97_100clusters_052515.nwk │ │ ├── ghosttree_UNITEv6_30.12.2014_97_80clusters_052515.nwk │ │ ├── ghosttree_UNITEv6_30.12.2014_99_100clusters_052515.nwk │ │ ├── ghosttree_UNITEv6_30.12.2014_99_80clusters_052515.nwk │ │ ├── ghosttree_UNITEv6_30.12.2014_dynamic_100clusters_052515.nwk │ │ └── ghosttree_UNITEv6_30.12.2014_dynamic_80clusters_052515.nwk │ ├── ghosttree_SILVA_SSU_119_UNITEv6_dynamic_s_100.nwk │ └── ghosttree_SILVA_SSU_119_UNITEv6_dynamic_s_80.nwk └── trees_021915_silva119_foundation_unite_ghost_trees │ ├── 0116 │ ├── 97_100_ghost_tree │ │ ├── ghost_tree.nwk │ │ └── ghost_tree_extension_accession_ids.txt │ └── 97_80_ghost_tree │ │ ├── ghost_tree.nwk │ │ └── ghost_tree_extension_accession_ids.txt │ ├── 0116_s │ ├── 97_100_ghost_tree │ │ ├── ghost_tree.nwk │ │ └── ghost_tree_extension_accession_ids.txt │ ├── 97_80_ghost_tree │ │ ├── ghost_tree.nwk │ │ └── ghost_tree_extension_accession_ids.txt │ ├── dynamic_100_ghost_tree │ │ ├── ghost_tree.nwk │ │ └── ghost_tree_extension_accession_ids.txt │ └── dynamic_80_ghost_tree │ │ ├── ghost_tree.nwk │ │ └── ghost_tree_extension_accession_ids.txt │ ├── 0815 │ ├── 99_100_ghost_tree │ │ ├── ghost_tree.nwk │ │ └── ghost_tree_extension_accession_ids.txt │ ├── 99_80_ghost_tree │ │ ├── ghost_tree.nwk │ │ └── ghost_tree_extension_accession_ids.txt │ ├── dynamic_100_ghost_tree │ │ ├── ghost_tree.nwk │ │ └── ghost_tree_extension_accession_ids.txt │ └── dynamic_80_ghost_tree │ │ ├── ghost_tree.nwk │ │ └── ghost_tree_extension_accession_ids.txt │ ├── 0815_s │ ├── 97_100_ghost_tree │ │ ├── 97_100_ghost-tree │ │ │ ├── ghost_tree.nwk │ │ │ └── ghost_tree_extension_accession_ids.txt │ │ └── 97_100_otu_map.txt │ ├── 97_80_ghost_tree │ │ ├── 97_80_ghost-tree │ │ │ ├── ghost_tree.nwk │ │ │ └── ghost_tree_extension_accession_ids.txt │ │ └── 97_80_otu_map.txt │ ├── 99_100_ghost_tree │ │ ├── 99_100_ghost-tree │ │ │ ├── ghost_tree.nwk │ │ │ └── ghost_tree_extension_accession_ids.txt │ │ └── 99_100_otu_map.txt │ ├── 99_80_ghost_tree │ │ ├── 99_80_ghost-tree │ │ │ ├── ghost_tree.nwk │ │ │ └── ghost_tree_extension_accession_ids.txt │ │ └── 99_80_otu_map.txt │ ├── dynamic_100_ghost_tree │ │ ├── dynamic_100_ghost_tree │ │ │ ├── ghost_tree.nwk │ │ │ └── ghost_tree_extension_accession_ids.txt │ │ └── dynamic_100_otu_map.txt │ └── dynamic_80_ghost_tree │ │ ├── dynamic_80_ghost_tree │ │ ├── ghost_tree.nwk │ │ └── ghost_tree_extension_accession_ids.txt │ │ └── dynamic_80_otu_map.txt │ ├── alpha_97 │ ├── 97_100_ghost_tree │ │ ├── ghost_tree.nwk │ │ └── ghost_tree_extension_accession_ids.txt │ └── 97_80_ghost_tree │ │ ├── ghost_tree.nwk │ │ └── ghost_tree_extension_accession_ids.txt │ └── alpha_99 │ ├── 99_100_ghost-tree │ ├── ghost_tree.nwk │ └── ghost_tree_extension_accession_ids.txt │ └── 99_80_ghost-tree │ ├── ghost_tree.nwk │ └── ghost_tree_extension_accession_ids.txt └── workflow ├── ghost-tree_workflow.ipynb ├── large_ghost_tree_demo_files ├── extensions_otu_map.txt └── foundation_alignment_file.txt ├── preprint_analyses ├── biom_tables │ ├── otu_table_even100.biom │ ├── otu_table_even100_filtered.biom │ └── otu_table_even100_filtered_n10_d0.6.biom ├── commands_for_preprint.txt ├── mapping_files │ ├── mappingfileSALIVAENV2.txt │ └── mappingfileSALIVAENV2_n10_d0.6.txt └── principal_coordinates │ ├── binary_jaccard_otu_table_even100_filtered_n10_d0.6_dm.txt │ ├── bray_curtis_otu_table_even100_filtered_n10_d0.6_dm.txt │ ├── ghost_tree_unweighted_unifrac_pc.txt │ └── ghost_tree_weighted_unifrac_pc.txt └── 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