Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences release_cr555dqdxfcjdgl5fdfsg6xnbm

by Arnaud Di Franco, Raphaël Poujol, Denis Baurain, Hervé Philippe

Published in BMC Evolutionary Biology by Springer Nature.

2019   Volume 19, Issue 1, p21

Abstract

Multiple Sequence Alignments (MSAs) are the starting point of molecular evolutionary analyses. Errors in MSAs generate a non-historical signal that can lead to incorrect inferences. Therefore, numerous efforts have been made to reduce the impact of alignment errors, by improving alignment algorithms and by developing methods to filter out poorly aligned regions. However, MSAs do not only contain alignment errors, but also primary sequence errors. Such errors may originate from sequencing errors, from assembly errors, or from erroneous structural annotations (such as incorrect intron/exon boundaries). Even though their existence is acknowledged, the impact of primary sequence errors on evolutionary inference is poorly characterized.
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