Phylogenetic tree (neighbour-joining, with bootstrap)

A neighbour-joining tree from a multiple ALIGNMENT, as Newick. Distances are corrected pairwise identities over the columns where both rows have a residue — Jukes-Cantor for nucleotides, Poisson for protein, the same corrections MEGA applies by default — and the tree is rooted at the midpoint of its longest tip-to-tip path. Branch support is Felsenstein's bootstrap over alignment columns, written into the Newick as the usual internal-node labels and returned per split; it needs four or more sequences and is refused with a reason past the work one call will do, rather than returned from fewer replicates under the same name. Takes the output of multiple_sequence_alignment: inferring an alignment here would bury the aligner's parameters inside a tree.