pylogeny.model module
Phylogenetic tree scoring models; intended to be coupled with the use of
pytbeaglehon (BEAGLE) high-performance library.
-
class pylogeny.model.DiscreteStateModel(alignment)[source]
Bases: object
Initialize a discrete state model
for phylogenetic data. State frequencies and character
time are determined from the given alignment object.
-
__init__(alignment)[source]
-
getAlignment()[source]
-
getAlignmentAsStateList()[source]
-
getCharType()[source]
-
getFrequencyOfState(i)[source]
-
getRawFrequencyOfState(i)[source]
-
getRawStateFreqs()[source]
-
getRawStateFreqsAsDict()[source]
-
getRawStateFreqsAsList()[source]
-
getSequenceMatrix()[source]
-
getStateFreqs()[source]
-
exception pylogeny.model.PhyloModelError(v)[source]
Bases: exceptions.Exception
-
__init__(v)[source]