phylo

Phylo is a module within Biopython that provides tools for working with phylogenetic trees. It focuses on representing evolutionary relationships and is designed to help researchers parse, manipulate, and visualize tree structures in Python. The module exposes a simple data model built around hierarchical nodes called Clades, which together form a tree with a designated root. Clades can carry attributes such as branch lengths, names, and posterior probabilities, and the API supports common operations such as traversal, pruning, and clade collapsing.

Phylo can read and write trees in standard formats used in phylogenetics, including Newick and Nexus, and it can handle other formats through optional parsers (for example PhyloXML and NeXML in certain distributions). The input/output functions accept file handles or strings and convert them into the internal tree representation, or vice versa. For visualization, Phylo offers simple ASCII rendering and basic plotting via matplotlib, enabling researchers to display trees with branch lengths and labels.

In practice, Phylo is used as part of the Biopython ecosystem to support phylogenetic analyses in computational workflows. It interoperates with other Biopython modules such as SeqIO for sequence data, AlignIO for alignments, and regular Python libraries for data analysis, enabling tasks from quick inspection of a tree to integration into larger analysis pipelines.

Phylo is maintained as an open-source project with a focus on readability and extensibility, reflecting the broader goals of Biopython to provide accessible tools for life-science researchers. See also: phylogenetics, Newick, Nexus, NeXML, PhyloXML, Biopython.