ivy.chars.catpars module

ivy.chars.catpars.ancstates(tree, chardata, stepmatrix)

Return parsimony ancestral states

Parameters:

• tree (Node) – Root of tree
• chardata (Dict) – Dict of tip labels mapping to character states
• stepmatrix (np.array) – Step matrix. Create default step matrix with default_costmatrix().

Returns:

Internal nodes mapping to reconstructed states.

Return type:

dict

ivy.chars.catpars.binary_deltran(tree, chardata, stepmatrix)

ivy.chars.catpars.default_costmatrix(numstates, dtype=<type 'int'>)

a square array with zeroes along the diagonal, ones elsewhere

ivy.chars.catpars.downpass(node, states, stepmatrix, chardata, node2dpv=None)

ivy.chars.catpars.minstates(v)

return the indices of v that equal the minimum

ivy.chars.catpars.uppass(node, states, stepmatrix, node2dpv, node2upm={}, node2ancstates=None)