dendropy.calculate.popgenstat: Population Genetics Statistics¶
Population genetic statistics.
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dendropy.calculate.popgenstat.average_number_of_pairwise_differences(char_matrix, ignore_uncertain=True)[source]¶ Returns $k$, calculated for a character block.
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dendropy.calculate.popgenstat.derived_state_matrix(char_matrix, ancestral_sequence=None, derived_state_alphabet=None, ignore_uncertain=True)[source]¶ Given a list of CharDataSequence objects, and a reference ancestral sequence, this returns a list of strings corresponding to the list of CharDataSequence objects, where a ‘0’ indicates the ancestral state and ‘1’ a derived state.
e.g.
- Given:
GGCTAATCTGA GCTTTTTCTGA GCTCTCTCTTC
- with ancestral sequence:
GGTTAATCTGA
- this returns:
0010000000 0000110000 0001110011
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dendropy.calculate.popgenstat.nucleotide_diversity(char_matrix, ignore_uncertain=True)[source]¶ Returns $pi$, calculated for a character block.
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dendropy.calculate.popgenstat.num_segregating_sites(char_matrix, ignore_uncertain=True)[source]¶ Returns the raw number of segregating sites (polymorphic sites).
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dendropy.calculate.popgenstat.tajimas_d(char_matrix, ignore_uncertain=True)[source]¶ Returns Tajima’s D.
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dendropy.calculate.popgenstat.unfolded_site_frequency_spectrum(char_matrix, ancestral_sequence=None, ignore_uncertain=False, pad=True)[source]¶ Returns the site frequency spectrum of list of CharDataSequence objects given by char_sequences, with reference to the ancestral sequence given by ancestral_seq. If ancestral_seq is None, then the first sequence in char_sequences is taken to be the ancestral sequence.
