CLUSTAL

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 17 articles )

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  1. Polishko, Anton; Hasan, Md. Abid; Pan, Weihua; Bunnik, Evelien M.; Le Roch, Karine; Lonardi, Stefano: ThIEF: finding genome-wide trajectories of epigenetics marks (2017)
  2. Axelson-Fisk, Marina: Comparative gene finding. Models, algorithms and implementation (2015)
  3. 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)
  4. Wang, Lei; Peng, Hui; Zheng, Jinhua: ADLD: a novel graphical representation of protein sequences and its application (2014)
  5. Daskalakis, Constantinos; Roch, Sebastien: Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis (2013)
  6. Andoni, Alexandr; Daskalakis, Constantinos; Hassidim, Avinatan; Roch, Sebastien: Global alignment of molecular sequences via ancestral state reconstruction (2012)
  7. Wolfsheimer, Stefan; Hartmann, Alexander; Rabus, Ralf; Nuel, Gregory: Computing posterior probabilities for score-based alignments using ppALIGN (2012)
  8. Bassoy, Cem Savas; Torgasin, Svetlana; Yang, Mei; Zimmermann, Karl-Heinz: Accelerating scalar-product based sequence alignment using graphics processor units (2010) ioport
  9. Kryukov, Kirill; Saitou, Naruya: MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data (2010) ioport
  10. Yue, Feng; Shi, Jian; Tang, Jijun: Simultaneous phylogeny reconstruction and multiple sequence alignment (2009) ioport
  11. Rosen, Gail; Garbarine, Elaine; Caseiro, Diamantino; Polikar, Robi; Sokhansanj, Bahrad: Metagenome fragment classification using (N)-mer frequency profiles (2008) ioport
  12. Pham, Tuan D.: Spectral distortion measures for biological sequence comparisons and database searching (2007)
  13. Xia, Xuhua: Bioinformatics and the cell. Modern computational approaches in genomics, proteomics and transcriptomics (2007)
  14. Zhang, Min; Fang, Weiwu; Zhang, Junhua; Chi, Zhongxian: MSAID: multiple sequence alignment based on a measure of information discrepancy (2005)
  15. Taylor, William R.: A non-local gap-penalty for profile alignment (1996)
  16. Wong, A. K. C.; Chan, S. C.; Chiu, D. K. Y.: A multiple sequence comparison method (1993)
  17. Chan, S. C.; Wong, A. K. C.; Chiu, D. K. Y.: A survey of multiple sequence comparison methods (1992)