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Issue: Vol. 4567 No. 2: 15 Mar. 2019
Type: Article
Published: 2019-03-15
DOI: 10.11646/zootaxa.4567.2.11
Page range: 387–394
Abstract views: 69
PDF downloaded: 4

Building combined MRP-matrices with BuM, an automated web-tool

Universidade Federal do ABC (Federal University of ABC), Santo André, SP, Brazil.
Universidade Federal do ABC (Federal University of ABC), Santo André, SP, Brazil.
Universidade Federal do ABC (Federal University of ABC), Santo André, SP, Brazil.
Universidade Federal do ABC (Federal University of ABC), Santo André, SP, Brazil.
Universidade Federal do ABC (Federal University of ABC), Santo André, SP, Brazil.
General cladistics MRP phylogeny supertrees topology

Abstract

The most common methods for combining different phylogenetic trees with uneven but overlapping taxon sampling are the Matrix Representation with Parsimony (MRP) and consensus tree methods. Although straightforward, some steps of MRP are time-consuming and risky when manually performed, especially the preparation of the matrix representations from the original topologies, and the creation of the single matrix containing all the information of the individual trees. Here we present Building MRP-Matrices (BuM), a free online tool for generating a combined matrix, following Baum and Ragan coding scheme, from files containing phylogenetic trees in parenthetical format.

 

References

  1. Baum, B.R. (1992) Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon, 41, 3–10.

    https://doi.org/10.2307/1222480

    Baum, B.R. & Ragan, M. (1993) Reply to A.G. Rodrigo’s “A comment on Baum’s method for combining phylogenetic trees”. Taxon, 42, 637–640.

    https://doi.org/10.2307/1222541

    Bininda-Emonds, O.R.P. (2010) The future of supertrees: bridging the gap with supermatrices. Paleodiversity, 3, 99–106.

    Bininda-Emonds, O.R.P., Cardillo, M., Jones, K.E., Macphee, R.D.E., Beck, R.M.D., Grenyer, R., Price, S.A., Vos, R.A., Gittleman, J.L. & Purvis, A. (2007) The delayed rise of present-day mammals. Nature, 446 (7135), 507–12.

    https://doi.org/10.1038/nature05634

    Goloboff, P.A. & Catalano, S.A. (2016) TNT version 1.5, including a full implementation of phylogenetic morphometrics. Cladistics, 32 (3), 221–238.

    https://doi.org/10.1111/cla.12160

    Goloboff, P.A., Farris, J.S. & Nixon, K.C. (2008) TNT, a free program for phylogenetic analysis. Cladistics, 24, 774–786.

    https://doi.org/10.1111/j.1096-0031.2008.00217.x

    Haeseler, A. (2012) Do we still need supertrees? BMC Biology, 10, 13–16.

    https://doi.org/10.1186/1741-7007-10-13

    Hill, J. & Davis, K.E. (2014) The Supertree Toolkit 2: a new and improved software package with a Graphical User Interface for supertree construction. Biodiversity Data Journal, 26 (2), e1053.

    https://doi.org/10.3897/BDJ.2.e1053

    Maddison, W.P. & Maddison, D.R. (2018) Mesquite: a modular system for evolutionary analysis. Version 3.51. Available from: http://www.mesquiteproject.org (accessed December 2018)

    Pisani, D. & Wilkinson, M. (2002) Matrix representations with parsimony, taxonomic congruence, and total evidence. Systematic Biology, 51 (1), 151–155.

    https://doi.org/10.1080/106351502753475925

    Ragan, M.A. (1992) Phylogenetic inference based on matrix representation of trees. Molecular Phylogenetics and Evolution, 1, 53–58.

    https://doi.org/10.1016/1055-7903(92)90035-F

    Revell, L.J. (2012) phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3 (2), 217–223.

    https://doi.org/10.1111/j.2041-210X.2011.00169.x

    Schliep, K.P. (2010) phangorn: phylogenetic analysis in R. Bioinformatics, 27 (4), 592–593.

    https://doi.org/10.1093/bioinformatics/btq706

    Swofford, D.L. (2002) PAUP*. Phylogenetic Analysis Using Parsimony (*and other Methods). Version 4. Sinauer Associates, Sunderland, USA.