Table 2. A comparison of execution times.

Number of sequences	Original NJ		New NJ
NJ algorithm only	Complete multiple alignment	NJ algorithm only	Complete multiple alignment
200	0′ 6″	0′ 11″	0.1″	0′ 5″
500	6′ 55″	7′ 27″	1.1″	0′ 33″
1000	XXX	XXX	16″	2′ 18″

A comparison of two different implementations of the NJ algorithm (not including the time taken for the calculation of the distance matrix) for different sizes of alignments. The time required for the NJ algorithm depends only on the number of sequences, while the complete multiple alignment depends also on the lengths of the sequences. The timings reported here were all performed for sequences of approximately ∼40 residues. XXX denotes the algorithm did not complete. The timings were performed on a Compaq Alpha EV67 running True64 UNIX.