Multiple sequence alignment is a core first step in many bioinformatics analyses, and errors in these alignments can have negative consequences for scientific studies. In this article, we review some of the recent literature evaluating multiple sequence alignment methods and identify specific challenges that arise when performing these evaluations. In particular, we discuss the different trends observed in simulation studies and when using biological benchmarks. Overall, we find that multiple sequence alignment, far from being a “solved problem,” would benefit from new attention.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages19
StatePublished - 2021

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Model misspecification
  • Multiple sequence alignment
  • Phylogeny estimation
  • Statistical alignment
  • Structural alignment

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology


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