title: Multiple sequence alignment modeling: methods and applications.
abstract: This review provides an overview on the development of Multiple sequence alignment (MSA) methods and their main applications. It is focused on progress made over the past decade. The three first sections review recent algorithmic developments for protein, RNA/DNA and genomic alignments. The fourth section deals with benchmarks and explores the relationship between empirical and simulated data, along with the impact on method developments. The last part of the review gives an overview on available MSA local reliability estimators and their dependence on various algorithmic properties of available methods.
authors.forename: Maria
authors.initials: M
authors.lastname: Chatzou
authors.forename: Cedrik
authors.initials: C
authors.lastname: Magis
authors.forename: Jia-Ming
authors.initials: JM
authors.lastname: Chang
authors.forename: Carsten
authors.initials: C
authors.lastname: Kemena
authors.forename: Giovanni
authors.initials: G
authors.lastname: Bussotti
authors.forename: Ionas
authors.initials: I
authors.lastname: Erb
authors.forename: Cedric
authors.initials: C
authors.lastname: Notredame
mesh_terms: D000465:Algorithms; D004247:DNA; D023281:Genomics; D011506:Proteins; D015203:Reproducibility of Results; D016415:Sequence Alignment
chemical_list: D011506:Proteins; D004247:DNA
keywords: DNA alignments; RNA alignments; alignment benchmarks; alignment reliability measures; multiple sequence alignments; protein alignments