Quality assessment of multiple alignment programs

Timo Lassmann, Erik L.L. Sonnhammer

Research output: Contribution to journalShort surveypeer-review

121 Citations (Scopus)


A renewed interest in the multiple sequence alignment problem has given rise to several new algorithms. In contrast to traditional progressive methods, computationally expensive score optimization strategies are now predominantly employed. We systematically tested four methods (Poa, Dialign, T-Coffee and ClustalW) for the speed and quality of their alignments. As test sequences we used structurally derived alignments from BAliBASE and synthetic alignments generated by Rose. The tests included alignments of variable numbers of domains embedded in random spacer sequences. Overall, Dialign was the most accurate in cases with low sequence identity, while T-Coffee won in cases with high sequence identity. The fast Poa algorithm was almost as accurate, while ClustalW could compete only in strictly global cases with high sequence similarity.

Original languageEnglish
Pages (from-to)126-130
Number of pages5
JournalFEBS Letters
Issue number1
Publication statusPublished - 2 Oct 2002
Externally publishedYes


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