Version Compatibility

Reference examples tested with: BioPython 1.83+, scanpy 1.10+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Tree I/O

"Read and convert my phylogenetic tree files" → Parse trees from Newick, Nexus, PhyloXML, or NeXML formats and convert between formats for use in different tools.

• Python: Bio.Phylo.read('tree.nwk', 'newick'), Bio.Phylo.convert()

Parse, write, and convert phylogenetic tree files in various formats.

Required Import