Index

_

__call__() (evolver.Evolver method)

A

AminoAcid_Matrix (class in matrix_builder)

assign_name() (model.Model method)

B

branch_het() (partition.Partition method)

C

compute_frequencies() (state_freqs.EmpiricalModelFrequencies method) (state_freqs.StateFrequencies method)

CustomFrequencies (class in state_freqs)

E

ECM_Matrix (class in matrix_builder) EmpiricalModelFrequencies (class in state_freqs) EqualFrequencies (class in state_freqs) Evolver (class in evolver) evolver (module)

extract_mutation_rates() (model.Model method) extract_parameters() (model.Model method) extract_rate_matrix() (model.Model method) extract_state_freqs() (model.Model method)

G

Genetics (class in genetics) genetics (module)

get_sequences() (evolver.Evolver method)

I

is_codon_model() (partition.Partition method)

is_hetcodon_model() (model.Model method)

M

matrix_builder (module) MatrixBuilder (class in matrix_builder) MechCodon_Matrix (class in matrix_builder)

Model (class in model) model (module) MutSel_Matrix (class in matrix_builder)

N

newick (module) Node (class in newick)

Nucleotide_Matrix (class in matrix_builder) num_classes() (model.Model method)

P

Partition (class in partition) partition (module)

print_tree() (in module newick)

R

RandomFrequencies (class in state_freqs) read_tree() (in module newick)

ReadFrequencies (class in state_freqs)

S

Site (class in evolver) site_het() (partition.Partition method)

state_freqs (module) StateFrequencies (class in state_freqs)