Criscuolo A, Gribaldo S (2010) BMGE (Block Mapping and Gathering with Entropy): selection of phylogenetic informative regions from multiple sequence alignments. BMC Evolutionary Biology 10:210.
BMGE (Block Mapping and Gathering with Entropy) is a program that selects regions in a multiple sequence alignment that are suited for phylogenetic inference. BMGE selects characters that are biologically relevant, thanks to the use of standard similarity matrices such as PAM or BLOSUM. Moreover, BMGE provides other character- or sequence-removal operations, such stationary-based character trimming (that provides a subset of compositionally homogeneous characters) or removal of sequences containing a too large proportion of gaps. Finally, BMGE can simply be used to perform standard conversion operations among DNA-, codon-, RY- and amino acid-coding sequences.