Index

_

__init__() (gctree.branching_processes.CollapsedForest method) (gctree.branching_processes.CollapsedTree method) (gctree.isotyping.Isotype method) (gctree.isotyping.IsotypeTemplate method) (gctree.mutation_model.MutationModel method)

A

add_isotypes() (gctree.branching_processes.CollapsedForest method), [1] (gctree.CollapsedForest method)

C

CollapsedForest (class in gctree) (class in gctree.branching_processes), [1] CollapsedTree (class in gctree) (class in gctree.branching_processes), [1]

compare() (gctree.branching_processes.CollapsedTree method), [1] (gctree.CollapsedTree method)

E

explode_idmap() (in module gctree.isotyping), [1]

F

feature_colormap() (gctree.branching_processes.CollapsedTree method), [1] (gctree.CollapsedTree method)

filter_trees() (gctree.branching_processes.CollapsedForest method), [1] (gctree.CollapsedForest method)

G

gctree.branching_processes module gctree.isotyping module

gctree.mutation_model module gctree.utils module

H

hamming_distance() (in module gctree.utils), [1]

I

Isotype (class in gctree.isotyping), [1] isotype (gctree.isotyping.Isotype attribute), [1] isotype_distance() (in module gctree.isotyping), [1] isotype_parsimony() (in module gctree.isotyping), [1]

isotype_tree() (in module gctree.isotyping), [1] IsotypeTemplate (class in gctree.isotyping), [1] iter_topology_classes() (gctree.branching_processes.CollapsedForest method), [1] (gctree.CollapsedForest method)

L

likelihood_rankplot() (gctree.branching_processes.CollapsedForest method), [1] (gctree.CollapsedForest method) ll() (gctree.branching_processes.CollapsedForest method), [1] (gctree.branching_processes.CollapsedTree method), [1] (gctree.CollapsedForest method) (gctree.CollapsedTree method)

local_branching() (gctree.branching_processes.CollapsedTree method), [1] (gctree.CollapsedTree method)

M

mle() (gctree.branching_processes.CollapsedForest method), [1] (gctree.branching_processes.CollapsedTree method), [1] (gctree.CollapsedForest method) (gctree.CollapsedTree method) module gctree.branching_processes gctree.isotyping gctree.mutation_model gctree.utils

mutabilities() (gctree.mutation_model.MutationModel method), [1] mutability() (gctree.mutation_model.MutationModel method), [1] mutate() (gctree.mutation_model.MutationModel method), [1] MutationModel (class in gctree.mutation_model), [1]

N

n_topologies() (gctree.branching_processes.CollapsedForest method), [1] (gctree.CollapsedForest method) n_trees (gctree.branching_processes.CollapsedForest attribute), [1] (gctree.CollapsedForest attribute)

new() (gctree.isotyping.IsotypeTemplate method), [1] newick() (gctree.branching_processes.CollapsedTree method), [1] (gctree.CollapsedTree method)

O

order (gctree.isotyping.Isotype attribute), [1]

P

parameters (gctree.branching_processes.CollapsedForest attribute), [1] (gctree.CollapsedForest attribute)

product() (in module gctree.utils)

R

RankingCriterionError, [1] render() (gctree.branching_processes.CollapsedTree method), [1] (gctree.CollapsedTree method)

resolutions() (gctree.isotyping.Isotype method), [1]

S

sample_tree() (gctree.branching_processes.CollapsedForest method), [1] (gctree.CollapsedForest method) simulate() (gctree.branching_processes.CollapsedForest method), [1] (gctree.branching_processes.CollapsedTree method), [1] (gctree.CollapsedForest method) (gctree.CollapsedTree method) (gctree.mutation_model.MutationModel method), [1]

support() (gctree.branching_processes.CollapsedTree method), [1] (gctree.CollapsedTree method)

T

tree (gctree.branching_processes.CollapsedTree attribute), [1] (gctree.CollapsedTree attribute)

W

weight_matrix (gctree.isotyping.Isotype attribute), [1]

write() (gctree.branching_processes.CollapsedTree method), [1] (gctree.CollapsedTree method)