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Evol Bioinform Online. 2016 Nov 28;12:277-284. eCollection 2016.

EvalMSA: A Program to Evaluate Multiple Sequence Alignments and Detect Outliers.

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Joint Research Unit "Infection and Public Health" FISABIO, Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Valencia, Spain.; CIBER in Epidemiology and Public Health, Madrid, Spain.


We present EvalMSA, a software tool for evaluating and detecting outliers in multiple sequence alignments (MSAs). This tool allows the identification of divergent sequences in MSAs by scoring the contribution of each row in the alignment to its quality using a sum-of-pair-based method and additional analyses. Our main goal is to provide users with objective data in order to take informed decisions about the relevance and/or pertinence of including/retaining a particular sequence in an MSA. EvalMSA is written in standard Perl and also uses some routines from the statistical language R. Therefore, it is necessary to install the R-base package in order to get full functionality. Binary packages are freely available from Linux and Windows.


gappiness; multiple sequence alignment; outlier sequence

Conflict of interest statement

Authors disclose no potential conflicts of interest.

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