AliStat version 1.3

AliStat has been written to allow users to evaluate how complete their multiple sequence alignments (MSA) of nucleotides or amino acids are.In particular, AliStat allows a user to generate four useful metrics (i.e. the completeness of an MSA (Ca), of a row in an MSA (Cr), of a column in an MSA (Cc), and of homologous sites in a sub-alignment of sequences i and j (Cij)), each of which will tell the user something useful about the distribution of missing data in an MSA.The information thus obtained can be used to make educated decisions about how the data in the MSA should be analysed phylogenetically.The output is a set of informative figures, tables, and sub-alignments.In addition, AliStat produces information that meets the Minimum Reporting Standard (MRS) for MSAs, a concept that we introduce in Wong TFK, Kalyaanamoorthy S, Meusemann K, Yeates DK, Misof B, Jermiin LS. 2017. AliStat: Quality-control metrics for multiple sequence alignments. Nature Methods (in prep).