pylogeny.scoring module¶

Functions for phylogenetic tree goodness-of-fit scoring.

pylogeny.scoring.beaglegetLogLikelihood(tree, alignment)[source]¶

Acquire log-likelihood via C++ library BEAGLE via use of pybeaglethon wrapper library. Currently uses HKY85 model.

Parameters:	tree (`tree.tree`) – A tree object. alignment (`alignment.alignment`) – An alignment object.
Returns:	A floating point value.

pylogeny.scoring.getLogLikelihood(tree, alignment, updateBranchLengths=True)[source]¶

Acquire log-likelihood via C library libpll. Requires the input alignment to be “Phylip friendly” (a phylipFriendlyAlignment).

Parameters:	tree (`tree.tree`) – A tree object. alignment (`alignment.phylipFriendlyAlignment`) – An alignment object. updateBranchLengths – Whether or not to update the branch lengths

in the provided tree with optimized ones. :returns: A floating point value.

pylogeny.scoring.getParsimony(newick, alignment)[source]¶

Acquire parsimony via a C++ implementation.

Parameters:	newick – A New Hampshire (Newick) tree string. alignment (`alignment.alignment`) – An alignment object.
Returns:	An integer value.

pylogeny.scoring.getParsimonyForTopology(topo, alignment)[source]¶

Acquire parsimony via a C++ implementation.

Parameters:	topo (`rearrangement.topology`) – A topology object. alignment (`alignment.alignment`) – An alignment object.
Returns:	An integer value.

pylogeny.scoring.getParsimonyFromProfiles(newick, profiles)[source]¶

Acquire parsimony via a C++ implementation.

Parameters:	newick – A New Hampshire (Newick) tree string. profiles (`parsimony.profile_set`) – A set of profiles corresponding to an alignment.
Returns:	An integer value.

pylogeny.scoring.getParsimonyFromProfilesForTopology(topology, profiles)[source]¶

Acquire parsimony via a C++ implementation.

Parameters:	topo (`rearrangement.topology`) – A topology object. profiles (`parsimony.profile_set`) – A set of profiles corresponding to an alignment.
Returns:	An integer value.