historydag.sequence_dag

Classes

AmbiguousLeafSequenceHistoryDag(dagroot[, attr])	A HistoryDag subclass with node labels containing full nucleotide sequences.
SequenceHistoryDag(dagroot[, attr])	A HistoryDag subclass with node labels containing full, unambiguous nucleotide sequences.

class historydag.sequence_dag.SequenceHistoryDag(dagroot, attr={})

A HistoryDag subclass with node labels containing full, unambiguous nucleotide sequences.

The constructor for this class requires that each node label contain a ‘sequence’ field, which is expected to hold an unambiguous nucleotide sequence.

A HistoryDag containing ‘compact_genome’ node label fields which contain compact_genome.CompactGenome objects may be automatically converted to this subclass by calling the class method SequenceHistoryDag.from_dag(), providing the HistoryDag object to be converted.

hamming_parsimony_count()

Count the hamming parsimony scores of all trees in the history DAG.

Returns a Counter with integer keys.

summary()

Print summary info about the history DAG.

class historydag.sequence_dag.AmbiguousLeafSequenceHistoryDag(dagroot, attr={})

A HistoryDag subclass with node labels containing full nucleotide sequences.

The constructor for this class requires that each node label contain a ‘sequence’ field, which is expected to hold an unambiguous nucleotide sequence if the node is internal. The sequence may be ambiguous for leaf nodes.

A HistoryDag containing ‘compact_genome’ node label fields which contain compact_genome.CompactGenome objects may be automatically converted to this subclass by calling the class method SequenceHistoryDag.from_dag(), providing the HistoryDag object to be converted.

hamming_parsimony_count()

Count the hamming parsimony scores of all trees in the history DAG.

Returns a Counter with integer keys.

summary()

Print summary info about the history DAG.