bio-phylo-distance-calculations

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.

Required Import

from Bio import Phylo, AlignIO
from Bio.Phylo.TreeConstruction import DistanceCalculator, DistanceTreeConstructor
from Bio.Phylo.TreeConstruction import DistanceMatrix
from Bio.Phylo.TreeConstruction import ParsimonyScorer, ParsimonyTreeConstructor, NNITreeSearcher
from Bio.Phylo.Consensus import strict_consensus, majority_consensus, bootstrap_trees, bootstrap_consensus

Distance Matrix from Alignment

from Bio import AlignIO
from Bio.Phylo.TreeConstruction import DistanceCalculator

alignment = AlignIO.read('alignment.fasta', 'fasta')

# Create calculator with distance model
calculator = DistanceCalculator('identity')  # Simple identity-based distance
dm = calculator.get_distance(alignment)
print(dm)

# Available models for DNA
calculator = DistanceCalculator('blastn')  # BLASTN-style distance

# Available models for protein
calculator = DistanceCalculator('blosum62')  # BLOSUM62-based distance

Available Distance Models

Model	Type	Description
identity	DNA/Protein	1 - (identical positions / total)
blastn	DNA	BLASTN scoring distance
trans	DNA	Transition/transversion weighted
blosum62	Protein	BLOSUM62 matrix distance
blosum45	Protein	BLOSUM45 matrix distance
blosum80	Protein	BLOSUM80 matrix distance
pam250	Protein	PAM250 matrix distance
pam30	Protein	PAM30 matrix distance