Tree I/O Reference

Import path

from phylognn.io import TreeReadConfig, read_tree_as_ete3

Optional dependency boundary

Core workflows use ete3.Tree directly. phylognn.io is the explicit optional boundary for DendroPy-backed file reading and conversion. Install the beast or all extra before using DendroPy readers.

Reader configuration

class TreeReadConfig(schema='nexus', tree_index=0, preserve_underscores=True, extract_comment_metadata=True, rooting=None, keep_annotations=True, annotation_prefix='meta_'): Frozen configuration for DendroPy-backed tree reading.

Reader functions

read_tree_as_ete3(file_path, schema='nexus', tree_index=0, preserve_underscores=True, extract_comment_metadata=True, rooting=None, keep_annotations=True, annotation_prefix='meta_'): Read one tree from a file and return an ete3.Tree.

read_tree_with_dendropy(file_path, config): Read one DendroPy tree from a file using TreeReadConfig.

dendropy_tree_to_ete3(dtree, config=None): Convert a DendroPy tree to an ete3.Tree.

Common failures

Missing DendroPy raises ModuleNotFoundError with install guidance. Invalid paths raise FileNotFoundError. Invalid tree indexes and empty files raise ValueError. Parser failures are wrapped in RuntimeError.