TrimAl: a tool for automated alignment trimming

Multiple sequence alignments (MSA) are central to many areas of bioinformatics and evolutionary biology. They are not only used in the phylogenetic analyses of biological sequences but also in many other bioinformatics applications such as homology modeling, database searchers and motif finding. Recently, such multiple sequence alignment based techniques have been incorporated in high-throughput pipelines such as genome annotation and large-scale phylogenetics. In all these applications the reliability and accuracy of the analyses depend critically on the quality of the underlying alignments. trimAl has been implemented in C++ programming language. So far a command-line version to download and a web interface are available.