Multiple sequence alignment modeling: methods and applications.

Authors :: Chatzou M
Magis C
Chang JM
Kemena C
Bussotti G
Erb I
Notredame C
Source :: Briefings in bioinformatics [Brief Bioinform] 2016 Nov; Vol. 17 (6), pp. 1009-1023. Date of Electronic Publication: 2015 Nov 27.
Publication Year :: 2016
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.<br /> (© The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.)