Build model-corrected evolutionary distance matrices and distance trees (NJ, BIONJ, FastME, UPGMA) with Biopython Bio.Phylo plus R ape/phangorn/FastME. Covers why a distance is a model-corrected estimate of substitutions per site that undercounts raw because of multiple/back/parallel hits (saturation); why the matrix discards the per-site information ML keeps; the LogDet/paralinear fix for compositional heterogeneity; the UPGMA molecular-clock trap; and the Bio.Phylo landmine that DistanceCalculator offers only identity/matrix distances, not JC/K80/TN93. Use when computing a distance matrix, building a fast NJ/FastME tree, seeding an ML search, barcoding, or testing subst…
