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CMAPLE 1.0.0
C++ MAximum Parsimonious Likelihood Estimation
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This is the complete list of members for cmaple::Tree, including all inherited members.
| applySPR(const TreeSearchType tree_search_type, const bool shallow_tree_search, std::ostream &out_stream=std::cout) | cmaple::Tree | |
| BIN_TREE enum value | cmaple::Tree | |
| changeAln(Alignment *aln) | cmaple::Tree | |
| changeModel(Model *model) | cmaple::Tree | |
| computeBranchSupport(const int num_threads=1, const int num_replicates=1000, const double epsilon=0.1, const bool allow_replacing_ML_tree=true, std::ostream &out_stream=std::cout) | cmaple::Tree | |
| computeLh() | cmaple::Tree | |
| doPlacement(std::ostream &out_stream=std::cout) | cmaple::Tree | |
| EXHAUSTIVE_TREE_SEARCH enum value | cmaple::Tree | |
| exportNewick(const TreeType tree_type=BIN_TREE, const bool show_branch_supports=true) | cmaple::Tree | |
| FAST_TREE_SEARCH enum value | cmaple::Tree | |
| infer(const TreeSearchType tree_search_type=NORMAL_TREE_SEARCH, const bool shallow_tree_search=false, std::ostream &out_stream=std::cout) | cmaple::Tree | |
| load(std::istream &tree_stream, const bool fixed_blengths=false) | cmaple::Tree | |
| load(const std::string &tree_filename, const bool fixed_blengths=false) | cmaple::Tree | |
| MUL_TREE enum value | cmaple::Tree | |
| NORMAL_TREE_SEARCH enum value | cmaple::Tree | |
| optimizeBranch(std::ostream &out_stream=std::cout) | cmaple::Tree | |
| Tree(Alignment *aln, Model *model, std::istream &tree_stream, const bool fixed_blengths=false, std::unique_ptr< cmaple::Params > &¶ms=nullptr) | cmaple::Tree | |
| Tree(Alignment *aln, Model *model, const std::string &tree_filename="", const bool fixed_blengths=false, std::unique_ptr< cmaple::Params > &¶ms=nullptr) | cmaple::Tree | |
| TreeSearchType enum name | cmaple::Tree | |
| TreeType enum name | cmaple::Tree | |
| UNKNOWN_TREE enum value | cmaple::Tree | |
| UNKNOWN_TREE_SEARCH enum value | cmaple::Tree | |
| ~Tree() | cmaple::Tree |
1.9.8