title: AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments.
abstract: 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 AlignStat.Science.LaTrobe.edu.au. The R package, readme and example data are available on CRAN and GitHub.com/TS404/AlignStat.
authors: Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Australia. T.Shafee@LaTrobe.edu.au.
authors: Thomas
authors: http://orcid.org/0000-0002-2298-7593
authors: T
authors: Shafee
authors: Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Australia.|Department of Molecular and Cell Biology, James Cook University, Townsville, 4811, Australia.
authors: Ira
authors: I
authors: Cooke
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software