OD-seq is a practical and simple method to detect outliers in MSAs. It can also detect outliers in sets of unaligned sequences, but with reduced accuracy.
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OD-seq: outlier detection in multiple sequence alignments.
Jehl P, Sievers F, Higgins DG.
BMC Bioinformatics. 2015 Aug 25;16:269. doi: 10.1186/s12859-015-0702-1.