BMGE

BMGE (Block Mapping and Gathering with Entropy) 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 sequenceremoval 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. more at BMGE manual (/usr/local/bmge/latest/doc/BMGE_doc.pdf)


References in zbMATH (referenced in 3 articles )

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  1. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  2. Heaps, Sarah E.; Nye, Tom M. W.; Boys, Richard J.; Williams, Tom A.; Embley, T. Martin: Bayesian modelling of compositional heterogeneity in molecular phylogenetics (2014)
  3. Jones, Martin O.; Koutsovoulos, Georgios D.; Blaxter, Mark L.: Iphy: an integrated phylogenetic workbench for supermatrix analyses (2011) ioport