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| PhyloTree (std::string filename) |
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| PhyloTree (const std::vector< std::string > &speciesnames, double b=1) |
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| PhyloTree (const PhyloTree &other) |
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void | getBranchLengths (std::vector< double > &branchset) const |
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void | scaleTree (double factor) |
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double | getDiversity () |
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void | getSpeciesNames (std::vector< std::string > &speciesnames) |
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int | numSpecies () |
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Treenode * | getLeaf (std::string species) const |
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void | printTree () const |
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void | printNewick (std::string filename) const |
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void | recursiveNWK (std::ofstream &file, Treenode *node) const |
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void | drop (std::string species) |
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void | drop (Treenode *node, Evo *evo) |
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void | collapse (Treenode *node, Evo *evo) |
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void | prune (bit_vector &bv, Evo *evo) |
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double | pruningAlgor (std::string labelpattern, Evo *evo, int u=0) |
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double | pruningAlgor (std::vector< int > &tuple, Evo *evo, int u=0) |
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void | printRecursionTable () const |
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double | MAP (std::vector< int > &labels, std::vector< double > &weights, Evo *evo, bool fixLeafLabels=false) |
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void | MAPbacktrack (std::vector< int > &labels, Treenode *root, int bestAssign, bool fixLeafLabels) |
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int | fitch (vector< int > &labels, int states=64) |
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static double | phylo_factor =1 |
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The documentation for this class was generated from the following files:
