API Reference

Base

from_ancestry	Convert an "ancestry matrix" to a vector
from_edges	Convert a list of edges to a Phylo2Vec vector
from_newick	Convert a Newick string to a Phylo2Vec vector or matrix
from_pairs	Convert a list of pairs to a Phylo2Vec vector
to_ancestry	Convert a Phylo2Vec vector to an ancestry matrix
to_edges	Convert a Phylo2Vec vector to an edge list
to_newick	Convert a Phylo2Vec vector or matrix to Newick format
to_pairs	Convert a Phylo2Vec vector to a list of pairs

IO

load	Read a text/csv file into a Phylo2Vec vector or matrix.
load_newick	Read a Newick string/file into a Phylo2Vec vector or matrix.
save	Save a Phylo2Vec vector or matrix to a file.
save_newick	Save a Phylo2Vec vector or matrix to Newick format into a file.

Statistics

stats.cophenetic_distances	Compute the cophenetic distance matrix of a Phylo2Vec vector (topological) or matrix (from branch lengths).
stats.cov	Compute the covariance matrix of a Phylo2Vec vector or matrix.
stats.incidence	Compute the incidence matrix of a Phylo2Vec vector.
stats.pairwise_distances	Compute a pairwise distance matrix for tree nodes from a Phylo2Vec vector.
stats.precision	Compute the precision matrix of a Phylo2Vec vector or matrix.
stats.robinson_foulds	Compute the Robinson-Foulds distance between two trees.

Utils

sample_matrix	Sample a random tree with branch lengths via Phylo2Vec, in matrix form.
sample_vector	Sample a random tree via Phylo2Vec, in vector form.
utils.matrix.check_matrix	Input validation of a Phylo2Vec matrix
utils.newick.apply_label_mapping	Apply an integer-taxon label mapping (label_mapping) from a string-based newick (where leaves are strings) and produce a mapped integer-based newick (where leaves are integers)
utils.newick.create_label_mapping	Create an integer-taxon label mapping (label_mapping) from a string-based newick (where leaves are strings) and produce a mapped integer-based newick (where leaves are integers) this also remove annotations pertaining to parent nodes
utils.newick.find_num_leaves	Calculate the number of leaves in a tree from its Newick
utils.newick.remove_branch_lengths	Remove branch lengths annotations from a Newick string
utils.newick.remove_parent_labels	Remove parent labels from the Newick string
utils.vector.add_leaf	Add a leaf to a Phylo2Vec vector v
utils.vector.check_vector	Input validation of a Phylo2Vec vector
utils.vector.get_common_ancestor	Get the most recent common ancestor between two nodes in a Phylo2Vec tree.
utils.vector.get_node_depth	Get the depth of a node in a Phylo2Vec tree.
utils.vector.get_node_depths	Get the depths of all nodes in a Phylo2Vec tree.
utils.vector.queue_shuffle	Produce an ordered version (i.e., birth-death process version) of a Phylo2Vec vector using the Queue Shuffle algorithm.
utils.vector.remove_leaf	Remove a leaf from a Phylo2Vec v
utils.vector.reroot	Reroot a tree in phylo2vec format at a given node
utils.vector.reroot_at_random	Reroot a tree in phylo2vec format at a random node