Sequence utilities / Phylogenetic tree (neighbour joining)
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Neighbour joining (NJ) repeatedly joins the closest branches according to pairwise distances, giving an approximate minimum-evolution tree; branch lengths are estimated substitutions (per site for nucleotides).
The tree itself is unrooted. “Midpoint rooting” places the root halfway along the longest leaf-to-leaf path for readability; this is not necessarily the true ancestral position. Use an outgroup if you have one.
Distance models: p-distance is the simple proportion of differences; JC69 and K2P correct for multiple substitutions (K2P separates transitions and transversions); proteins use the Poisson correction by default. Very divergent pairs saturate and cannot be corrected.
No bootstrap test is performed, so branch support should be assessed separately; copy the Newick output into the tree viewer tool for colouring and styling.
Neighbour joining: Saitou & Nei 1987 (Mol Biol Evol 4:406); Studier & Keppler 1988; JC69: Jukes & Cantor 1969; K2P: Kimura 1980 (J Mol Evol 16:111). Topology and branch lengths match Biopython DistanceTreeConstructor.nj.
Up to 50 sequences of up to 2,000 residues when alignment is needed; up to 500 taxa from an alignment or distance matrix.
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