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

BMC Evolutionary Biology
Alexis Criscuolo, Simonetta Gribaldo

Abstract

The quality of multiple sequence alignments plays an important role in the accuracy of phylogenetic inference. It has been shown that removing ambiguously aligned regions, but also other sources of bias such as highly variable (saturated) characters, can improve the overall performance of many phylogenetic reconstruction methods. A current scientific trend is to build phylogenetic trees from a large number of sequence datasets (semi-)automatically extracted from numerous complete genomes. Because these approaches do not allow a precise manual curation of each dataset, there exists a real need for efficient bioinformatic tools dedicated to this alignment character trimming step. 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...Continue Reading

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Citations

Sep 8, 2011·Heredity·A D Twyford, R A Ennos
Jun 12, 2012·Genome Biology and Evolution·Philippe Deschamps, David Moreira
Jun 10, 2011·Molecular Biology and Evolution·Alexis Criscuolo, Simonetta Gribaldo
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Software Mentioned

MP
Seq
BMGE
BioNJ
MUSCLE
Gen
TNT
BLOSUM95
Noisy
LogDet

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