BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

Here is presented a new software, named BMGE (Block Mapping and Gathering with Entropy), that is designed to select regions in a multiple sequence alignment that are suited for phylogenetic inference. For each character, BMGE computes a score closely related to an entropy value. Calculation of these entropy-like scores is weighted with BLOSUM or PAM similarity matrices in order to distinguish among biologically expected and unexpected variability for each aligned character. Sets of contiguous characters with a score above a given threshold are considered as not suited for phylogenetic inference and then removed. Simulation analyses show that the character trimming performed by BMGE produces datasets leading to accurate trees, especially with alignments including distantly-related sequences. BMGE also implements trimming and recoding methods aimed at minimizing phylogeny reconstruction artefacts due to compositional heterogeneity.BMGE is able to perform biologically relevant trimming on a multiple alignment of DNA, codon or amino acid sequences. Java source code and executable are freely available at ftp://ftp.pasteur.fr/pub/GenSoft/projects/BMGE/ webcite.Most phylogenetic inference approaches are based on an alignment of homologous sequences (e.g. DNA, RNA, amino acids). The alignment of sequences aims at highlighting the substitutions that have occurred during the evolutionary process from their common ancestral sequence. The quality of a multiple sequence alignment can have a strong impact on the accuracy of the inferred phylogenetic tree, whatever the inference criterion used [1-4]. In spite of constant improvements of the multiple sequence alignment heuristics [5,6], an alignment can contain regions (i.e. sets of contiguous characters, also often called blocks [7,8]) where homology is ambiguous. Moreover, too divergent regions (even when correctly aligned) may induce a mutational saturation effect, which is an important source of bias for many phylogenetic recon