A toolkit for working with phylogenetic data.
v0.22.1
File List
Here is a list of all files with brief descriptions:
 accumulator.cppImplementation of Histogram Accumulator class
 accumulator.hppHeader of Histogram Accumulator class
 algorithm.hppProvides some valuable algorithms that are not part of the C++ 11 STL
 attributes.cpp
 attributes.hpp
 balances.cpp
 balances.hpp
 base_input_source.hpp
 bipartition.hpp
 bitmap.cpp
 bitmap.hpp
 bitvector.cppImplementation of bitvector functions
 bitvector.hpp
 block.cpp
 block.hpp
 broker.cppImplementation of NewickBroker class
 broker.hpp
 char.hpp
 char_lookup.hpp
 circular_layout.cpp
 circular_layout.hpp
 codes.cpp
 codes.hpp
 cog.cpp
 cog.hpp
 col.hpp
 color.cpp
 color.hppHeader of Color class
 color_bar.cpp
 color_bar.hpp
 color_writer_plugin.hpp
 newick/color_writer_plugin.hpp
 phyloxml/color_writer_plugin.hpp
 common.hpp
 compact.cpp
 compact.hpp
 consensus.cpp
 consensus.hpp
 convert.hpp
 counts.cpp
 counts.hpp
 dataframe.cpp
 containers/dataframe.hpp
 math/regression/dataframe.hpp
 date_time.cppImplementation of date and time functions
 date_time.hppProvides functions for date and time access
 definitions.hpp
 deref_iterator.hpp
 deserializer.hppHeader of Serializer and Deserializer class
 detailed.cpp
 detailed.hpp
 distance.cpp
 distance.hpp
 placement/function/distances.cpp
 tree/common_tree/distances.cppImplementation of CommonTree distance methods
 tree/function/distances.cppImplementation of Tree distance methods
 utils/math/histogram/distances.cppImplementation of Histogram distance functions
 placement/function/distances.hpp
 tree/common_tree/distances.hppHeader of CommonTree distance methods
 tree/function/distances.hppHeader of Tree distance methods
 utils/math/histogram/distances.hppHeader of Histogram distance functions
 distributions.cpp
 distributions.hpp
 diverging_lists.cpp
 diverging_lists.hpp
 json/document.cpp
 nexus/document.cpp
 svg/document.cpp
 xml/document.cppImplementation of XML document functions
 json/document.hpp
 nexus/document.hpp
 svg/document.hpp
 xml/document.hppA collection of classes for working with XML documents. See XmlDocument for more
 edge.hpp
 placement/formats/edge_color.cpp
 tree/common_tree/edge_color.cpp
 placement/formats/edge_color.hpp
 tree/common_tree/edge_color.hpp
 edge_data.hpp
 element.hpp
 placement/function/emd.cpp
 tree/mass_tree/emd.cpp
 placement/function/emd.hpp
 tree/mass_tree/emd.hpp
 sequence/functions/entropy.cpp
 taxonomy/functions/entropy.cpp
 sequence/functions/entropy.hpp
 taxonomy/functions/entropy.hpp
 entropy_data.hpp
 epca.cpp
 epca.hpp
 euclidean_kmeans.cpp
 euclidean_kmeans.hpp
 eulertour.hpp
 factor.hpp
 family.hpp
 fasta_input_iterator.hpp
 fasta_output_iterator.hpp
 fasta_reader.cpp
 fasta_reader.hpp
 fasta_writer.cpp
 fasta_writer.hpp
 file_input_source.hpp
 fs.cppImplementation of file system functions
 fs.hppProvides functions for accessing the file system
 placement/function/functions.cppImplementation of the Placement Functions
 placement/simulator/functions.cpp
 sequence/functions/functions.cpp
 tree/bipartition/functions.cppImplementation of BipartitionSet class
 tree/common_tree/functions.cppImplementation of Common Tree functions
 tree/drawing/functions.cpp
 tree/function/functions.cpp
 tree/mass_tree/functions.cpp
 utils/math/twobit_vector/functions.cpp
 utils/tools/color/functions.cppColor operators and functions
 utils/tools/geodesy/functions.cpp
 utils/tools/hash/functions.cpp
 placement/function/functions.hppProvides functions for working with Placements and Pqueries
 placement/simulator/functions.hpp
 sequence/functions/functions.hpp
 tree/bipartition/functions.hpp
 tree/common_tree/functions.hppCommonTree functions
 tree/drawing/functions.hpp
 tree/function/functions.hpp
 tree/mass_tree/functions.hpp
 utils/math/twobit_vector/functions.hpp
 utils/tools/color/functions.hppColor operators and functions
 utils/tools/geodesy/functions.hpp
 utils/tools/hash/functions.hpp
 genesis.hpp
 geo_coordinate.hpp
 glm.cpp
 glm.hpp
 gradient.cpp
 gradient.hpp
 group.cpp
 group.hpp
 gzip.cpp
 gzip.hpp
 gzip_input_source.cpp
 gzip_input_source.hpp
 heat_tree.cpp
 heat_tree.hpp
 placement/function/helper.cppImplementation of the Placement Functions
 utils/formats/xml/helper.cpp
 utils/math/regression/helper.cpp
 placement/function/helper.hpp
 utils/formats/svg/helper.hpp
 utils/formats/xml/helper.hpp
 utils/math/regression/helper.hpp
 helpers.cpp
 helpers.hpp
 histogram.cppImplementation of Histogram class
 histogram.hppHeader of Histogram class
 image.cpp
 image.hpp
 indexed_newick_reader.cppImplementation of NewickBroker class
 indexed_newick_reader.hpp
 input_buffer.hpp
 tree/formats/newick/input_iterator.hpp
 utils/formats/csv/input_iterator.hpp
 input_reader.hpp
 input_source.hpp
 input_stream.hpp
 iterator.hpp
 iterator_deletions.hpp
 iterator_insertions.hpp
 iterator_substitutions.hpp
 jplace_reader.cpp
 jplace_reader.hpp
 jplace_writer.cpp
 jplace_writer.hpp
 keyed_newick_reader.cppImplementation of NewickBroker class
 keyed_newick_reader.hpp
 kmeans.cpp
 tree/mass_tree/kmeans.hpp
 utils/math/kmeans.hpp
 labels.cpp
 labels.hpp
 layout_base.cpp
 layout_base.hpp
 layout_tree.hpp
 lca_lookup.cpp
 lca_lookup.hpp
 taxonomy/iterator/levelorder.hpp
 tree/iterator/levelorder.hpp
 tree/tree/link.hpp
 utils/math/regression/link.hpp
 logging.cppImplementation of Logging functions
 logging.hppProvides easy and fast logging functionality
 placement/function/manipulation.cpp
 tree/function/manipulation.cpp
 placement/function/manipulation.hpp
 tree/function/manipulation.hpp
 map.cpp
 map.hpp
 masses.cppImplementation of the Placement Functions
 masses.hpp
 formats/svg/matrix.cpp
 math/matrix.cpp
 containers/matrix.hpp
 formats/svg/matrix.hpp
 math/matrix.hpp
 md5.cpp
 md5.hpp
 mds.cpp
 mds.hpp
 measures.cppImplementation of PlacementMeasures class
 measures.hppHeader for Placement Measures functions
 mru_cache.hpp
 name.hpp
 names.cpp
 names.hpp
 ncbi.cpp
 ncbi.hpp
 nested.cppImplementation of Taxonomy class
 nested.hpp
 placement/formats/newick_reader.hpp
 tree/common_tree/newick_reader.hpp
 placement/formats/newick_writer.hpp
 tree/common_tree/newick_writer.hpp
 nhd.cpp
 nhd.hpp
 node.hpp
 node_data.hpp
 node_links.hpp
 norm_boundary.hpp
 norm_diverging.hpp
 norm_linear.hpp
 norm_logarithmic.hpp
 normalization.hpp
 object.hpp
 operations.cppImplementation of Histogram operations functions
 operations.hppHeader of Histogram operations functions
 placement/function/operators.cpp
 tree/common_tree/operators.cpp
 tree/function/operators.cppImplementation of Tree operator functions
 utils/containers/dataframe/operators.cpp
 utils/containers/matrix/operators.cpp
 utils/math/bitvector/operators.cpp
 utils/math/histogram/operators.cppImplementation of Histogram operator functions
 placement/function/operators.hpp
 taxonomy/functions/operators.hpp
 tree/common_tree/operators.hpp
 tree/function/operators.hppTree operator functions
 utils/containers/dataframe/operators.hpp
 utils/containers/matrix/operators.hppMatrix operators
 utils/math/bitvector/operators.hpp
 utils/math/histogram/operators.hppHeader of Histogram operator functions
 options.cppImplementation of Options members
 options.hpp
 output_stream.hpp
 parser.cpp
 parser.hpp
 path.hpp
 path_set.hpp
 pca.cpp
 pca.hpp
 phylip_reader.cpp
 phylip_reader.hpp
 phylip_writer.cpp
 phylip_writer.hpp
 phylo_factor.cpp
 phylo_factor.hpp
 phylo_factor_colors.cpp
 phylo_factor_colors.hpp
 phylo_ilr.cpp
 phylo_ilr.hpp
 phyloxml_writer.hpp
 placement/pquery/placement.hppHeader of PqueryPlacement class
 placement.hpp
 placement_tree.hpp
 plain.hppHeader of PqueryPlain class
 taxonomy/iterator/postorder.hpp
 tree/iterator/postorder.hpp
 pquery.cppImplementation of Pquery class
 pquery.hpp
 taxonomy/iterator/preorder.hpp
 tree/iterator/preorder.hpp
 qualitative_lists.cpp
 qualitative_lists.hpp
 random.cpp
 random.hpp
 range.hpp
 range_minimum_query.cpp
 range_minimum_query.hpp
 ranking.hpp
 ranks.cpp
 ranks.hpp
 tree/formats/newick/reader.cpp
 utils/formats/csv/reader.cpp
 utils/formats/json/reader.cpp
 tree/formats/newick/reader.hpp
 utils/containers/dataframe/reader.hpp
 utils/containers/matrix/reader.hpp
 utils/formats/csv/reader.hpp
 utils/formats/json/reader.hpp
 rectangular_layout.cpp
 rectangular_layout.hpp
 row.hpp
 sample.cppImplementation of Sample class
 sample.hpp
 sample_set.cpp
 function/sample_set.hpp
 sample_set.hpp
 scanner.hpp
 sequence/sequence.hpp
 sequence.hpp
 sequence_set.cppImplementation of SequenceSet class
 sequence_set.hpp
 sequential_lists.cpp
 sequential_lists.hpp
 serializer.cppImplementation of SampleSerializer class
 placement/formats/serializer.hppHeader of SampleSerializer class
 utils/io/serializer.hppHeader of Serializer and Deserializer class
 sha1.cpp
 sha1.hpp
 sha256.cpp
 sha256.hpp
 shapes.cpp
 shapes.hpp
 signature_specifications.cpp
 signature_specifications.hpp
 signatures.cpp
 signatures.hpp
 simple.cpp
 simple.hpp
 simulator.cppImplementation of Placement Simulator class
 simulator.hpp
 slr.hpp
 squash_clustering.cpp
 squash_clustering.hpp
 statistics.hpp
 sequence/functions/stats.cpp
 utils/math/histogram/stats.cppImplementation of Histogram statistics functions
 sequence/functions/stats.hpp
 utils/math/histogram/stats.hppHeader of Histogram statistics functions
 std.hppProvides some valuable additions to STD
 stream_input_source.hpp
 string.cppImplementation of string utility functions
 string.hppProvides some commonly used string utility functions
 string_input_source.hpp
 style.cpp
 style.hpp
 subtree.hpp
 svg.hpp
 tree/printer/table.cpp
 utils/text/table.cpp
 tree/printer/table.hpp
 utils/text/table.hpp
 taxa.hpp
 taxon.cppImplementation of Taxon class
 taxon.hpp
 taxon_data.hpp
 functions/taxonomy.cpp
 taxonomy.cppImplementation of Taxonomy class
 taxonomy/functions/taxonomy.hpp
 taxonomy/taxonomy.hpp
 taxonomy.hpp
 taxonomy_reader.cpp
 taxonomy_reader.hpp
 taxonomy_writer.cpp
 taxonomy_writer.hpp
 taxopath.cpp
 functions/taxopath.hpp
 taxopath.hpp
 taxopath_generator.cppImplementation of TaxopathGenerator class
 taxopath_generator.hpp
 taxopath_parser.cppImplementation of TaxopathParser class
 taxopath_parser.hpp
 text.cpp
 text.hpp
 tickmarks.cpp
 tickmarks.hpp
 placement/function/tree.cpp
 taxonomy/functions/tree.cpp
 tree/tree.cppImplementation of Tree class
 placement/function/tree.hpp
 taxonomy/functions/tree.hpp
 tree/attribute_tree/tree.hpp
 tree/common_tree/tree.hpp
 tree/mass_tree/tree.hpp
 tree/tree.hppHeader of Tree class
 tree.hpp
 tree_set.cpp
 function/tree_set.hpp
 tree_set.hpp
 trees.hpp
 twobit_vector.cpp
 twobit_vector.hpp
 utils.hpp
 version.hppSome stuff that is totally not imporatant, but nice
 tree/formats/newick/writer.cpp
 tree/formats/phyloxml/writer.cppImplementation of functions for reading and writing Phyloxml files
 utils/formats/bmp/writer.cpp
 utils/formats/json/writer.cpp
 utils/formats/nexus/writer.cpp
 utils/formats/xml/writer.cpp
 tree/formats/newick/writer.hpp
 tree/formats/phyloxml/writer.hpp
 utils/containers/matrix/writer.hpp
 utils/formats/bmp/writer.hpp
 utils/formats/json/writer.hpp
 utils/formats/nexus/writer.hpp
 utils/formats/xml/writer.hpp