Glossary

Alias

An alternative, shorter command name. For example, aln_len is an alias for alignment_length and dispatches to the same implementation.

Bipartition

A split of the taxa induced by removing an edge from a phylogenetic tree.

Canonical command

The stable, descriptive command name used for its reference page and primary machine-readable identity.

Cladogram

A tree drawing that emphasizes topology and does not interpret branch lengths as evolutionary distance or time.

Gene tree discordance

Differences among gene-tree topologies or between gene trees and a species tree.

Handler

The Python function that implements a canonical command and its aliases.

Newick

A parenthetical plain-text representation of a phylogenetic tree.

Patristic distance

The sum of branch lengths along the path between two tree tips.

Phylogenetic signal

Statistical dependence between trait similarity and phylogenetic relatedness. Individual statistics such as Blomberg's K and Pagel's lambda have distinct definitions and interpretations.

Phylogram

A tree drawing in which branch lengths represent an estimated amount of change.

Polytomy

An internal node with more than two immediate descendants, often representing unresolved relationships.

Standalone executable

A pk_* command installed for a canonical command or alias, such as pk_alignment_length or pk_aln_len.

Taxon

A named unit represented by an alignment record, tree tip, or trait-table row.

TSV

A tab-separated values file. Tabs delimit columns; spaces are not equivalent.

VCV matrix

A phylogenetic variance-covariance matrix describing expected covariance among taxa under an evolutionary model.