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.
Some programs such as G-blocks have been developed to assist in the alignment trimming phase, by selecting blocks of conserved regions in the alignment. However their use in large-scale analyses is hampered by the need of defining, prior to the analysis, a set of parameters that will be used in all sequence families. Here we present trimAl, a tool for automated alignment trimming, which is especially suited for large-scale analyses. Its speed and the possibility for automatically adjusting the parameters to optimize the phylogenetic signal-to-noise ratios for different families, makes trimAl especially suited for large-scale phylogenomic analyses, involving thousands of large multiple sequence alignments.
trimAl has been implemented in C++ programming language. So far a command-line version to download and a web interface are available.
One of the main problems that the researchers have to face during their studies is the conversion among the various formats required by different programs. Nowadays there around 20 different Multiple Sequence Alignment (MSAs) formats. Here we present readAl, a tool for format alignment conversion among the most representative formats. readAl has been designed to be used in several situations, including, alignment trimming, phylogenetic tree reconstruction, profile reconstruction, and so on.
readAl has been implemented in C++ programming language. This program is part of the trimAl package and is used internally by trimAl to convert among different formats. Moreover, you can find a readAl webserver version.