DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. Background: DIALIGN-T is a reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets than previous versions of DIALIGN. However, like the original implementation of the program, DIALIGN-T uses a a straight-forward greedy approach to assemble multiple alignments from local pairwise sequence similarities. Such greedy approaches may be vulnerable to spurious random similarities and can therefore lead to suboptimal results. In this paper, we present DIALIGN-TX, a substantial improvement of DIALIGN-T that combines our previous greedy algorithm with a progressive alignment approach.

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  1. DeBlasio, Dan; Kececioglu, John: Parameter advising for multiple sequence alignment (2017)
  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. Federico, Maria; Peterlongo, Pierre; Pisanti, Nadia; Sagot, Marie-France: \textscRime: repeat identification (2014)
  4. Didier, Gilles; Corel, Eduardo; Laprevotte, Ivan; Grossmann, Alex; Landès-Devauchelle, Claudine: Variable length local decoding and alignment-free sequence comparison (2012)
  5. Di Luccio, Eric; Koehl, Patrice: A quality metric for homology modeling: the H-factor (2011) ioport
  6. Kim, Jaebum; Sinha, Saurabh: Towards realistic benchmarks for multiple alignments of non-coding sequences (2010) ioport
  7. Schreiber, Fabian; Pick, Kerstin; Erpenbeck, Dirk; Wörheide, Gert; Morgenstern, Burkhard: Orthoselect: a protocol for selecting orthologous groups in phylogenomics (2009) ioport