A toolkit for working with phylogenetic data.
v0.18.0
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File List
Here is a list of all files with brief descriptions:
o*accumulator.cppImplementation of Histogram Accumulator class
o*accumulator.hppHeader of Histogram Accumulator class
o*algorithm.hppProvides some valuable algorithms that are not part of the C++ 11 STL
o*attributes.cpp
o*attributes.hpp
o*bipartition.hpp
o*bipartition_set.cppImplementation of BipartitionSet class
o*bipartition_set.hpp
o*bitmap.cpp
o*bitmap.hpp
o*bitvector.cppImplementation of bitvector functions
o*bitvector.hpp
o*block.cpp
o*block.hpp
o*broker.cppImplementation of NewickBroker class
o*broker.hpp
o*char.hpp
o*char_lookup.hpp
o*circular_layout.cpp
o*circular_layout.hpp
o*circular_tree.hpp
o*codes.cpp
o*codes.hpp
o*cog.cpp
o*cog.hpp
o*color.cpp
o*color.hppHeader of Color class
o*color_writer_plugin.hpp
o*newick/color_writer_plugin.hpp
o*phyloxml/color_writer_plugin.hpp
o*common.cpp
o*common.hpp
o*compact.cpp
o*compact.hpp
o*consensus.cpp
o*consensus.hpp
o*counts.cpp
o*counts.hpp
o*date_time.cppImplementation of date and time functions
o*date_time.hppProvides functions for date and time access
o*definitions.hpp
o*detailed.cpp
o*detailed.hpp
o*placement/pquery/distances.cpp
o*tree/default/distances.cppImplementation of Default Tree distance methods
o*tree/function/distances.cppImplementation of Tree distance methods
o*utils/math/histogram/distances.cppImplementation of Histogram distance functions
o*placement/pquery/distances.hpp
o*tree/default/distances.hppHeader of Default Tree distance methods
o*tree/function/distances.hppHeader of Tree distance methods
o*utils/math/histogram/distances.hppHeader of Histogram distance functions
o*distributions.cpp
o*distributions.hpp
o*json/document.cpp
o*nexus/document.cpp
o*svg/document.cpp
o*xml/document.cppImplementation of XML document functions
o*json/document.hpp
o*nexus/document.hpp
o*svg/document.hpp
o*xml/document.hppA collection of classes for working with XML documents. See XmlDocument for more
o*edge.cppImplementation of TreeEdge class
o*edge.hpp
o*placement/formats/edge_color.cpp
o*tree/default/edge_color.cpp
o*placement/formats/edge_color.hpp
o*tree/default/edge_color.hpp
o*edge_data.hpp
o*element.hpp
o*placement/function/emd.cpp
o*tree/mass_tree/emd.cpp
o*placement/function/emd.hpp
o*tree/mass_tree/emd.hpp
o*sequence/functions/entropy.cpp
o*taxonomy/functions/entropy.cpp
o*sequence/functions/entropy.hpp
o*taxonomy/functions/entropy.hpp
o*entropy_data.hpp
o*epca.cpp
o*epca.hpp
o*eulertour.hpp
o*fasta_input_iterator.hpp
o*fasta_output_iterator.hpp
o*fasta_reader.cpp
o*fasta_reader.hpp
o*fasta_writer.cpp
o*fasta_writer.hpp
o*fs.cppImplementation of file system functions
o*fs.hppProvides functions for accessing the file system
o*placement/function/functions.cppImplementation of the Placement Functions
o*placement/simulator/functions.cpp
o*sequence/functions/functions.cpp
o*tree/default/functions.cppImplementation of Default Tree functions
o*tree/function/functions.cpp
o*tree/mass_tree/functions.cpp
o*utils/math/twobit_vector/functions.cpp
o*utils/tools/color/functions.cppColor operators and functions
o*utils/tools/geodesy/functions.cpp
o*placement/function/functions.hppProvides functions for working with Placements and Pqueries
o*placement/simulator/functions.hpp
o*sequence/functions/functions.hpp
o*tree/default/functions.hppDefault Tree functions
o*tree/function/functions.hpp
o*tree/mass_tree/functions.hpp
o*utils/math/twobit_vector/functions.hpp
o*utils/tools/color/functions.hppColor operators and functions
o*utils/tools/geodesy/functions.hpp
o*genesis.hpp
o*geodesy.hpp
o*gradient.cpp
o*gradient.hpp
o*group.cpp
o*group.hpp
o*placement/function/helper.cppImplementation of the Placement Functions
o*utils/formats/xml/helper.cpp
o*placement/function/helper.hpp
o*utils/formats/svg/helper.hpp
o*utils/formats/xml/helper.hpp
o*histogram.cppImplementation of Histogram class
o*histogram.hppHeader of Histogram class
o*image.cpp
o*image.hpp
o*indexed_list.hppHeader of IndexedList class
o*indexed_newick_reader.cppImplementation of NewickBroker class
o*indexed_newick_reader.hpp
o*inorder.hpp
o*input_buffer.hpp
o*input_iterator.hpp
o*input_reader.hpp
o*input_source.hpp
o*input_stream.hpp
o*iterator.hpp
o*iterator_deletions.hpp
o*iterator_insertions.hpp
o*iterator_substitutions.hpp
o*jplace_reader.cpp
o*jplace_reader.hpp
o*jplace_writer.cpp
o*jplace_writer.hpp
o*keyed_newick_reader.cppImplementation of NewickBroker class
o*keyed_newick_reader.hpp
o*tree/mass_tree/kmeans.cpp
o*utils/math/kmeans.cpp
o*tree/mass_tree/kmeans.hpp
o*utils/math/kmeans.hpp
o*labels.cpp
o*labels.hpp
o*layout_base.cpp
o*layout_base.hpp
o*layout_tree.hpp
o*lca_lookup.cpp
o*lca_lookup.hpp
o*taxonomy/iterator/levelorder.hpp
o*tree/iterator/levelorder.hpp
o*link.cppImplementation of TreeLink class
o*link.hpp
o*lists.cpp
o*lists.hpp
o*logging.cppImplementation of Logging functions
o*logging.hppProvides easy and fast logging functionality
o*manipulation.cpp
o*manipulation.hpp
o*matrix.hpp
o*measures.cppImplementation of PlacementMeasures class
o*measures.hppHeader for Placement Measures functions
o*name.cpp
o*name.hpp
o*names.cpp
o*names.hpp
o*nested.cppImplementation of Taxonomy class
o*nested.hpp
o*placement/formats/newick_reader.hpp
o*tree/default/newick_reader.hpp
o*placement/formats/newick_writer.hpp
o*tree/default/newick_writer.hpp
o*nhd.cpp
o*nhd.hpp
o*node.cppImplementation of TreeNode class
o*node.hpp
o*node_data.hpp
o*node_links.hpp
o*object.hpp
o*operations.cppImplementation of Histogram operations functions
o*operations.hppHeader of Histogram operations functions
o*placement/function/operators.cpp
o*tree/default/operators.cpp
o*tree/function/operators.cppImplementation of Tree operator functions
o*utils/math/histogram/operators.cppImplementation of Histogram operator functions
o*utils/math/matrix/operators.cpp
o*placement/function/operators.hpp
o*taxonomy/functions/operators.hpp
o*tree/default/operators.hpp
o*tree/function/operators.hppTree operator functions
o*utils/containers/sorted_vector/operators.hpp
o*utils/math/histogram/operators.hppHeader of Histogram operator functions
o*utils/math/matrix/operators.hppMatrix operators
o*options.cppImplementation of Options members
o*options.hpp
o*output_stream.hpp
o*palette.cpp
o*palette.hpp
o*parser.cpp
o*parser.hpp
o*path.hpp
o*path_set.hpp
o*pca.cpp
o*pca.hpp
o*phylip_reader.cpp
o*phylip_reader.hpp
o*phylip_writer.cpp
o*phylip_writer.hpp
o*phyloxml_writer.hpp
o*placement.cppImplementation of PqueryPlacement class
o*placement/pquery/placement.hppHeader of PqueryPlacement class
o*placement.hpp
o*placement_tree.cppImplementation of PlacementTree class
o*placement_tree.hpp
o*plain.hppHeader of PqueryPlain class
o*taxonomy/iterator/postorder.hpp
o*tree/iterator/postorder.hpp
o*pquery.cppImplementation of Pquery class
o*pquery.hpp
o*taxonomy/iterator/preorder.hpp
o*tree/iterator/preorder.hpp
o*random.cpp
o*random.hpp
o*range.hpp
o*range_minimum_query.cpp
o*range_minimum_query.hpp
o*ranks.cpp
o*ranks.hpp
o*tree/formats/newick/reader.cpp
o*utils/formats/csv/reader.cpp
o*utils/formats/json/reader.cpp
o*tree/formats/newick/reader.hpp
o*utils/formats/csv/reader.hpp
o*utils/formats/json/reader.hpp
o*utils/math/matrix/reader.hpp
o*rectangular_layout.cpp
o*rectangular_layout.hpp
o*rectangular_tree.hpp
o*sample.cppImplementation of Sample class
o*sample.hpp
o*function/sample_set.cpp
o*sample_set.cppImplementation of SampleSet class
o*function/sample_set.hpp
o*sample_set.hpp
o*scanner.hpp
o*sequence.cppImplementation of Sequence class
o*sequence/sequence.hpp
o*sequence.hpp
o*sequence_set.cppImplementation of SequenceSet class
o*sequence_set.hpp
o*serializer.cppImplementation of SampleSerializer class
o*placement/formats/serializer.hppHeader of SampleSerializer class
o*utils/io/serializer.hppHeader of Serializer and Deserializer class
o*sha1.cpp
o*sha1.hpp
o*shapes.cpp
o*shapes.hpp
o*signatures.cpp
o*signatures.hpp
o*simple.cpp
o*simple.hpp
o*simulator.cppImplementation of Placement Simulator class
o*simulator.hpp
o*sorted_vector.hpp
o*squash_clustering.cpp
o*squash_clustering.hpp
o*statistics.cpp
o*statistics.hppMatrix statstic functions
o*sequence/functions/stats.cpp
o*utils/math/histogram/stats.cppImplementation of Histogram statistics functions
o*sequence/functions/stats.hpp
o*utils/math/histogram/stats.hppHeader of Histogram statistics functions
o*std.hppProvides some valuable additions to STD
o*string.cppImplementation of string utility functions
o*string.hppProvides some commonly used string utility functions
o*style.cpp
o*style.hpp
o*svg.hpp
o*tree/printer/table.cpp
o*utils/text/table.cpp
o*tree/printer/table.hpp
o*utils/text/table.hpp
o*taxa.hpp
o*taxon.cppImplementation of Taxon class
o*taxon.hpp
o*taxon_data.hpp
o*functions/taxonomy.cpp
o*taxonomy.cppImplementation of Taxonomy class
o*taxonomy/functions/taxonomy.hpp
o*taxonomy/taxonomy.hpp
o*taxonomy.hpp
o*taxonomy_reader.cpp
o*taxonomy_reader.hpp
o*functions/taxopath.cpp
o*taxopath.cppImplementation of Taxopath class
o*functions/taxopath.hpp
o*taxopath.hpp
o*taxopath_generator.cppImplementation of TaxopathGenerator class
o*taxopath_generator.hpp
o*taxopath_parser.cppImplementation of TaxopathParser class
o*taxopath_parser.hpp
o*text.cpp
o*text.hpp
o*tickmarks.cpp
o*tickmarks.hpp
o*placement/function/tree.cpp
o*tree/tree.cppImplementation of Tree class
o*placement/function/tree.hpp
o*tree/attribute_tree/tree.hpp
o*tree/default/tree.hpp
o*tree/mass_tree/tree.hpp
o*tree/tree.hppHeader of Tree class
o*tree.hpp
o*function/tree_set.cpp
o*tree_set.cppImplementation of TreeSet class
o*function/tree_set.hpp
o*tree_set.hpp
o*trees.hpp
o*twobit_vector.cpp
o*twobit_vector.hpp
o*utils.hpp
o*version.hppSome stuff that is totally not imporatant, but nice
o*tree/formats/newick/writer.cpp
o*tree/formats/phyloxml/writer.cppImplementation of functions for reading and writing Phyloxml files
o*utils/formats/bmp/writer.cpp
o*utils/formats/json/writer.cpp
o*utils/formats/nexus/writer.cpp
o*utils/formats/xml/writer.cpp
o*tree/formats/newick/writer.hpp
o*tree/formats/phyloxml/writer.hpp
o*utils/formats/bmp/writer.hpp
o*utils/formats/json/writer.hpp
o*utils/formats/nexus/writer.hpp
\*utils/formats/xml/writer.hpp