Table 1 

Complexity of CLUSTALW. Here we show the bigO asymptotic complexity of the elements of CLUSTALW as a function of L, the typical sequence length, and N, the number of sequences, retaining the highestorder terms in N with L fixed and vice versa. 

Step 
O(Space) 
O(Time) 


Distance matrix 
N^{2 }+ L 
N^{2}L^{2} 
Neighbor joining 
N^{2} 
N^{4} 
Progressive (one iteration) 
NL_{P }+ L_{P }= NL + L^{2} 
NL_{P }+ L_{P}^{2 }= N^{2 }+ L^{2} 
Progressive (total) 
NL + L^{2} 
N^{3 }+ NL^{2} 
TOTAL 
N^{2 }+ L^{2} 
N^{4 }+ L^{2} 


Edgar BMC Bioinformatics 2004 5:113 doi:10.1186/147121055113 