Salvador Capella Gutierrez.
Comparative Genomics Group. Bioinformatics & Genomics Programme. CRG
May, 11th at 11:30am, room 470.2
Multiple sequence alignments (MSA) are central to many areas of bioinformatics. The quality of downstream analyses depends on the accuracy of MSAs. For instance, it has been shown that removing conflicting regions from an alignment help to increase the quality of phylogenetic analysis. In large scale analyses THERE is a need to appropriately determine the best trimming parameters to each alignment. Here, we present trimAl, a tool for automated alignment trimming, which is especially suited for large-scale 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. Besides implementing the assessment and trimming of alignments, trimAl is an efficient format-conversion tool that eases the concatenation of different alignment-based analyses. In this tutorial, I will go over the main potentialities of trimAl, showing selected practical examples.
trimAl can be accessed at trimal.cgenomics.org
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