Pileup vs clustalW

Andrea Hansen webmaster at bioinformatik.de
Sun Oct 1 11:36:37 EST 2000

KeXueH at IOGEN.ca (KeXue Huang) writes:
> Hi, There,
> What is the difference between these two sequence alignment software:
> Pileup(GCG) and ClustalW? Does anybody tried the same sequence alignment
> using these two software? Thanks!

Pileup creates a multiple sequence alignment using a simplification of the progressive alignment method of Feng and Doolittle. The procedure begins with the pairwise alignment of the two most similar sequences, producing a cluster of two aligned sequences. This cluster will be aligned to the next most related sequence or cluster of sequences. The final alignment is achieved by a series of progressive, pairwise alignments.
Before alignment, the sequences are first clustered by similarity to produce a dendogram using the UPGMA method. ClustalW aligns the multiple sequences more accurately than Pileup because ClustalW use the Neighbor-joining method instead of UPGMA to cluster the sequences.
ClustalW use a more sophisticated alignment method than Pileup and produce a more robust alignment. The only time when differences between the programs won't be obvious is when the sequences are very similar to each other.


Institut fuer Botanik III    Tel +49 211 81 12339
Heinrich-Heine-Universitaet  Fax +49 211 81 13554
Universitaetsstr.1           email : webmaster at bioinformatik.de 
40225 Duesseldorf            http://www.bioinformatik.de

More information about the Methods mailing list