Pileup vs clustalW
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.
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