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AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments

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journal contribution
posted on 2021-01-20, 08:31 authored by Thomas ShafeeThomas Shafee, Ira CookeIra Cooke
© 2016 The Author(s). Background: Alternative sequence alignment algorithms yield different results. It is therefore useful to quantify the similarities and differences between alternative alignments of the same sequences. These measurements can identify regions of consensus that are likely to be most informative in downstream analysis. They can also highlight systematic differences between alignments that relate to differences in the alignment algorithms themselves. Results: Here we present a simple method for aligning two alternative multiple sequence alignments to one another and assessing their similarity. Differences are categorised into merges, splits or shifts in one alignment relative to the other. A set of graphical visualisations allow for intuitive interpretation of the data. Conclusions: AlignStat enables the easy one-off online use of MSA similarity comparisons or into R pipelines. The web-tool is available at The R package, readme and example data are available on CRAN and


TS was supported by the Australian Research Council. IC was supported by the Victorian Life Sciences Computation Initiative, a collaboration between Melbourne, Monash and La Trobe Universities and an initiative of the Victorian Government, Australia. The funding bodies had no further roles.

Australian Research Council

Victorian Life Sciences Computation Initiative

Victorian Government, Australia


Publication Date



BMC Bioinformatics





Article Number



6p. (p. 1-6)


BioMed Central



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