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Bioinformatics Advance Access originally published online on June 8, 2009
Bioinformatics 2009 25(15):1972-1973; doi:10.1093/bioinformatics/btp348
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

Salvador Capella-Gutiérrez , José M. Silla-Martínez and Toni Gabaldón *

Comparative Genomics group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88 08003 Barcelona, Spain

* To whom correspondence should be addressed.


  Abstract

Summary: Multiple sequence alignments are central to many areas of bioinformatics. It has been shown that the removal of poorly aligned regions from an alignment increases the quality of subsequent analyses. Such an alignment trimming phase is complicated in large-scale phylogenetic analyses that deal with thousands of alignments. Here, we present trimAl, a tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses. trimAl can consider several parameters, alone or in multiple combinations, for selecting the most reliable positions in the alignment. These include the proportion of sequences with a gap, the level of amino acid similarity and, if several alignments for the same set of sequences are provided, the level of consistency across different alignments. Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized.

Availability: trimAl has been written in C++, it is portable to all platforms. trimAl is freely available for download (http://trimal.cgenomics.org) and can be used online through the Phylemon web server (http://phylemon2.bioinfo.cipf.es/). Supplementary Material is available at http://trimal.cgenomics.org/publications.

Contact: tgabaldon{at}crg.es

Associate Editor: Martin Bishop

Received on May 27, 2008; revised on May 20, 2009; accepted on June 1, 2009

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