Search

Motivation: Multiple sequence alignments are generally reconstructed using a progressive approach that follows a guide-tree. During this process, gaps are introduced at a cost to maximize residue pairing, but it is unclear whether inferred gaps reflect actual past events of sequence insertions or deletions. It has been found that patterns of inferred gaps in alignments contain information towards the true phylogeny, but it is as yet unknown whether gaps are simply reflecting information that was already present in the guide-tree., Results: We here develop a framework to disentangle the phylogenetic signal carried by gaps from that which is already present in the guide-tree. Our results indicate that most gaps are incorrectly inserted in patterns that, nevertheless, follow the guide-tree. Thus, most gap patterns in current alignments are not informative per se. This affects different programs to various degrees, PRANK being the most sensitive to the guide-tree., Supplementary Information: Supplementary data are available at Bioinformatics online.

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.