A minimum reporting standard for multiple sequence alignments

Thomas K F Wong; Subha Kalyaanamoorthy; Karen Meusemann; David K Yeates; Bernhard Misof; Lars S Jermiin

doi:10.1093/nargab/lqaa024

A minimum reporting standard for multiple sequence alignments

NAR Genom Bioinform. 2020 Apr 14;2(2):lqaa024. doi: 10.1093/nargab/lqaa024. eCollection 2020 Jun.

Authors

Thomas K F Wong^{1

2}, Subha Kalyaanamoorthy^{1

3}, Karen Meusemann^{4

5

6}, David K Yeates⁴, Bernhard Misof⁵, Lars S Jermiin^{1

2

7

8}

Affiliations

¹ Land & Water, CSIRO, Canberra, ACT 2601, Australia.
² Research School of Biology, Australian National University, Canberra, ACT 2600, Australia.
³ Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
⁴ Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia.
⁵ Zoologisches Forschungsmuseum Alexander Koenig, 53113 Bonn, Germany.
⁶ Evolutionsbiologie & Ökologie, Institut für Biologie I, Albert-Ludwigs-Universität Freiburg, 79085 Freiburg im Breisgau, Germany.
⁷ School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
⁸ Earth Institute, University College Dublin, Belfield, Dublin 4 Ireland.

Abstract

Multiple sequence alignments (MSAs) play a pivotal role in studies of molecular sequence data, but nobody has developed a minimum reporting standard (MRS) to quantify the completeness of MSAs in terms of completely specified nucleotides or amino acids. We present an MRS that relies on four simple completeness metrics. The metrics are implemented in AliStat, a program developed to support the MRS. A survey of published MSAs illustrates the benefits and unprecedented transparency offered by the MRS.