Data

CassiopeiaTrees

The main data structure that Cassiopeia uses for all tree-based analyses is the CassiopeiaTree:

data.CassiopeiaTree([character_matrix, …])

Basic tree object for Cassiopeia.

Utilities

We also have several utilities that are useful for working with various data related to phylogenetics:

data.compute_dissimilarity_map(cm, C, …[, …])	Compute the dissimilarity between all samples
data.get_lca_characters(vecs, …)	Builds the character vector of the LCA of a list of character vectors, obeying Camin-Sokal Parsimony.
data.sample_bootstrap_allele_tables(allele_table)	Generates bootstrap character matrices from an allele table.
data.sample_bootstrap_character_matrices(…)	Generates bootstrapped character matrices from a character matrix.
data.to_newick(tree[, record_branch_lengths])	Converts a networkx graph to a newick string.

cassiopeia.pp.convert_lineage_profile_to_character_matrix cassiopeia.data.CassiopeiaTree