Multiple sequence alignment using probcons and probalign

Research output: Contribution to journalArticlepeer-review


Sequence alignment remains a fundamental task in bioinformatics. The literature contains programs that employ a host of exact and heuristic strategies available in computer science. Probcons was the first program to construct maximum expected accuracy sequence alignments with hidden Markov models and at the time of its publication achieved the highest accuracies on standard protein multiple alignment benchmarks. Probalign followed this strategy except that it used a partition function approach instead of hidden Markov models. Several programs employing both strategies have been published since then. In this chapter we describe Probcons and Probalign.

Original languageEnglish (US)
Pages (from-to)147-153
Number of pages7
JournalMethods in Molecular Biology
StatePublished - Jan 1 2014

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics


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