Estimating pair-wise distances. We use a general time reversible nucleotide substitution model (line 1). The pair-wise distances (line 4) are passed to the neighbor joining (nj) function (line 5), which returns a tree that is then written to file (line 6).
Knight et al. Genome Biology 2007 8:R171 doi:10.1186/gb-2007-8-8-r171