Journal Article

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

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

in Bioinformatics

Volume 25, issue 15, pages 1972-1973
Published in print August 2009 | ISSN: 1367-4803
Published online June 2009 | e-ISSN: 1460-2059 | DOI:

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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 ( and can be used online through the Phylemon web server ( Supplementary Material is available at


Journal Article.  1354 words. 

Subjects: Bioinformatics and Computational Biology

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