add_deletion	add_deletion
add_dropout	add_dropout
as_igraph	as_igraph
as_igraph,data.frame-method	as_igraph-data.frame-method
as_igraph,phylo-method	as_igraph-phylo-method
as_lineage_tree	as_lineage_tree
as_lineage_tree,phyDat,phylo,lineage_tree_config-method	as_lineage_tree-phyDat-phylo-lineage_tree_config-method
as_phylo	as_phylo
as_phylo,igraph-method	as_phylo-igraph-method
DCLEAR	DCLEAR
dist_kmer_replacement_inference	dist_kmer_replacement_inference
dist_replacement	dist_replacement
dist_replacement,phyDat,kmer_summary,integer-method	dist_replacement-phyDat-kmer_summary-integer-method
dist_replacement,phyDat,missing,integer-method	dist_replacement-phyDat-missing-integer-method
dist_weighted_hamming	dist_weighted_hamming
dist_weighted_hamming,phyDat,numeric-method	dist_weighted_hamming-phyDat-numeric-method
downsample	downsample
downsample,igraph-method	downsample-igraph-method
downsample,lineage_tree-method	downsample-lineage_tree-method
get_distance_prior	get_distance_prior
get_leaves	get_leaves
get_leaves,lineage_tree-method	get_leaves-lineage_tree-method
get_node_names	get_node_names
get_replacement_probability	get_replacement_probability
get_sequence	get_sequence
get_transition_probability	get_transition_probability
lineages	lineages
positional_mutation_prob	positional_mutation_prob
process_sequence	process_sequence
process_sequence,phyDat-method	process_sequence-phyDat-method
prune	prune
prune,igraph-method	prune-igraph-method
prune,lineage_tree-method	prune-lineage_tree-method
random_tree	random_tree
rbind,phyDat-method	rbind-phyDat-method
sample_mutation_outcome	sample_mutation_outcome
sample_mutation_site	sample_mutation_site
sample_outcome_prob	sample_outcome_prob
score_simulation	score_simulation
simulate	simulate
simulate,lineage_tree_config,missing-method	simulate-lineage_tree_config-missing-method
simulate,lineage_tree_config,phyDat-method	simulate-lineage_tree_config-phyDat-method
simulate_core	simulate_core
sim_seqdata	sim_seqdata
substr_kmer	substr_kmer
substr_kmer,kmer_summary-method	substr_kmer-kmer_summary-method
subtract	subtract
subtract,lineage_tree,lineage_tree-method	subtract-lineage_tree-lineage_tree-method
subtree	subtree
subtree,lineage_tree-method	subtree-lineage_tree-method
subtree,phylo-method	subtree-phylo-method
summarize_kmer	summarize_kmer
summarize_kmer,phyDat-method	summarize_kmer-phyDat-method
summarize_kmer_core	summarize_kmer_core
WH	WH
WH_train	WH_train
WH_train_fit	WH_train_fit
