CHANGELOG.rst
LICENSE
MANIFEST.in
README.rst
pyproject.toml
requirements.txt
tipp3/__init__.py
tipp3/configs.py
tipp3/default.config
tipp3/extract_blast_alignment.py
tipp3/init_configs.py
tipp3/jobs.py
tipp3/query_abundance.py
tipp3/query_alignment.py
tipp3/query_binning.py
tipp3/query_placement.py
tipp3/refpkg_loader.py
tipp3/tipp3_pipeline.py
tipp3.egg-info/PKG-INFO
tipp3.egg-info/SOURCES.txt
tipp3.egg-info/dependency_links.txt
tipp3.egg-info/entry_points.txt
tipp3.egg-info/requires.txt
tipp3.egg-info/top_level.txt
tipp3/helpers/__init__.py
tipp3/helpers/alignment_tools.py
tipp3/helpers/general_tools.py
tipp3/helpers/math_utils.py
tipp3/helpers/pyhmmer_tools.py
tipp3/tools/merge/build.xml
tipp3/tools/merge/tipp.xml
tipp3/tools/merge/tippJsonMerger.jar
tipp3/tools/merge/META-INF/MANIFEST.MF
tipp3/tools/merge/lib/commons-beanutils-1.8.3.jar
tipp3/tools/merge/lib/commons-collections-3.2.1.jar
tipp3/tools/merge/lib/commons-lang-2.6.jar
tipp3/tools/merge/lib/commons-logging-1.1.1.jar
tipp3/tools/merge/lib/ezmorph-1.0.6.jar
tipp3/tools/merge/lib/gson-1.7.1.jar
tipp3/tools/merge/lib/json-lib-2.4-jdk15.jar
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/algos/lca/SchieberVishkinLCA.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/BitVector.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/io/NewickReader.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/io/NewickWriter.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/io/ParseException.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/model/MutableTree.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/model/TMutableNode.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/model/TNode.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/model/Tree.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/model/sti/STINode.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/model/sti/STITree.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/model/sti/STITreeBipartition.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/model/sti/STITreeCluster.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/model/sti/STITreeClusterWD.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/util/Bipartitions.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/util/Collapse.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/util/PostTraversal.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/structs/tree/util/Trees.java
tipp3/tools/merge/src/edu/rice/cs/bioinfo/programs/phylonet/util/LIDAMath.java
tipp3/tools/merge/src/phylolab/NewickTokenizer.java
tipp3/tools/merge/src/phylolab/taxonamic/JSONMerger.java
tipp3/tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java
tipp3/tools/merge/src/phylolab/taxonamic/TaxonomyData.java
tipp3/tools/pplacer/pplacer