Version Compatibility

Reference examples tested with: BioPython 1.83+, NCBI BLAST+ 2.15+

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.

Distance Calculations and Tree Building

"Build a phylogenetic tree from my alignment" → Compute evolutionary distance matrices from sequence alignments and construct neighbor-joining or UPGMA trees with bootstrap support.

• Python: Bio.Phylo.TreeConstruction.DistanceCalculator(), DistanceTreeConstructor()

Compute distances from alignments and construct phylogenetic trees.

When to Use Distance Methods vs ML