BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
Gascuel O. Molecular Biology and Evolution. 1997 14:685-695.
papers if you use BIONJ.
A distance based phylogeny reconstruction algorithm
BIONJ is well suited for distances estimated from DNA or protein sequences. BIONJ has better topological accuracy than NJ in all evolutionary conditions; its superiority becomes important when the substitution rates are high and varying among lineages. However, BIONJ and NJ trees are often close or identical, notably when the number of taxa is low. BIONJ retains the speed of NJ and can be applied to very large data sets (> 1000 taxa). BIONJ can be run on several matrices to build bootstrap trees. As usual, distances should be corrected, e.g. using DNADIST or PROTDIST from PHYLIP.
BIONJ is available in PAUP
(4.0b10 and latter), and a PHYLIP compatible version can be downloaded from