CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. An approach for performing multiple alignments of large numbers of amino acid or nucleotide sequences is described. The method is based on first deriving a phylogenetic tree from a matrix of all pairwise sequence similarity scores, obtained using a fast pairwise alignment algorithm. Then the multiple alignment is achieved from a series of pairwise alignments of clusters of sequences, following the order of branching in the tree. The method is sufficiently fast and economical with memory to be easily implemented on a microcomputer, and yet the results obtained are comparable to those from packages requiring mainframe computer facilities.

References in zbMATH (referenced in 13 articles )

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  1. Axelson-Fisk, Marina: Comparative gene finding. Models, algorithms and implementation (2015)
  2. Mora-Gutiérrez, Roman Anselmo; Lárraga-Ramírez, María E.; Rincón-García, Eric A.; Ponsich, Antonin; Ramírez-Rodríguez, Javier: Adaptation of the method of musical composition for solving the multiple sequence alignment problem (2015)
  3. Daskalakis, Constantinos; Roch, Sebastien: Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis (2013)
  4. Andoni, Alexandr; Daskalakis, Constantinos; Hassidim, Avinatan; Roch, Sebastien: Global alignment of molecular sequences via ancestral state reconstruction (2012)
  5. Wolfsheimer, Stefan; Hartmann, Alexander; Rabus, Ralf; Nuel, Gregory: Computing posterior probabilities for score-based alignments using ppALIGN (2012)
  6. Bassoy, Cem Savas; Torgasin, Svetlana; Yang, Mei; Zimmermann, Karl-Heinz: Accelerating scalar-product based sequence alignment using graphics processor units (2010) ioport
  7. Rosen, Gail; Garbarine, Elaine; Caseiro, Diamantino; Polikar, Robi; Sokhansanj, Bahrad: Metagenome fragment classification using $N$-mer frequency profiles (2008) ioport
  8. Pham, Tuan D.: Spectral distortion measures for biological sequence comparisons and database searching (2007)
  9. Xia, Xuhua: Bioinformatics and the cell. Modern computational approaches in genomics, proteomics and transcriptomics (2007)
  10. Zhang, Min; Fang, Weiwu; Zhang, Junhua; Chi, Zhongxian: MSAID: multiple sequence alignment based on a measure of information discrepancy (2005)
  11. Taylor, William R.: A non-local gap-penalty for profile alignment (1996)
  12. Wong, A.K.C.; Chan, S.C.; Chiu, D.K.Y.: A multiple sequence comparison method (1993)
  13. Chan, S.C.; Wong, A.K.C.; Chiu, D.K.Y.: A survey of multiple sequence comparison methods (1992)