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

Álvaro ChinerOms | Zendy; Fernando GónzálezCandelas | Zendy

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

Author(s) -

Álvaro ChinerOms,

Fernando GónzálezCandelas

Publication year - 2016

Publication title -

evolutionary bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.502

H-Index - 32

ISSN - 1176-9343

DOI - 10.4137/ebo.s40583

Subject(s) - perl , computer science , outlier , identification (biology) , software , sequence (biology) , data mining , relevance (law) , r package , base (topology) , information retrieval , binary number , quality (philosophy) , data science , programming language , artificial intelligence , mathematical analysis , botany , genetics , mathematics , arithmetic , political science , law , biology , philosophy , epistemology

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 http://sourceforge.net/projects/evalmsa/for Linux and Windows.

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