Matteo Comin, University of Padova, Italy

Phylogenetic methods for biological sequences
Phylogenetics is the study of evolutionary relatedness among various groups of organisms (e.g., species, populations), which is discovered through molecular sequencing data and morphological data matrices. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa. In this tutorial we will describe the basic aspects involved in the computation of phylogenetic trees including methods based on: Distance-matrix, Maximum parsimony, Maximum likelihood and Bayesian inference. We will also discuss recent methods for alignment-free whole-genome phylogeny.

References

  1. Bioinformatics: Sequence and Genome Analysis
    David W. Mount
    Cold Spring Harbor Laboratory Press

  2. Molecular Systematics
    David M. Hillis, Craig Moritz, Barbara K. Mable
    Sinauer Associates, Inc.

  3. Biological Sequence Analysis.
    R. Durbin, S. Eddy, A. Krogh and G. Mitchison.
    Cambridge University Press

  4. Edwards, A. & Cavalli-Sforza, L. 1964.
    Reconstruction of evolutionary trees. Phenetic and Phylogenetic Classification.
    Systematics Association Publ. No. 6.

  5. Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions
    Gregory E. Sims, Se-Ran Jun, Guohong A. Wu, and Sung-Hou Kim,
    PNAS, vol. 106, no. 8, 2677–2682

  6. Whole-genome phylogeny of mammals: Evolutionary information in genic and nongenic regions
    Gregory E. Sims, Se-Ran Jun, Guohong Albert Wu, and Sung-Hou Kim,
    PNAS, vol. 106, no. 40, pp 17077–17082

  7. Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution
    Se-Ran Jun, Gregory E. Sims, Guohong A. Wu, and Sung-Hou Kim,
    PNAS, vol. 107, no. 1, 133–138

  8. Comparison of alignment free string distances for complete genome phylogeny
    Frédéric Guyon · Céline Brochier-Armanet · Alain Guénoche Advances
    in Data Analysis and Classification (2009) 3:95–108

  9. Information Theoretic Approaches to Whole Genome Phylogenies.
    Igor Ulitsky, David Burstein, Tamir Tuller, Benny Chor
    Proceeding of Research in Computational Molecular Biology (RECOMB)
    Lecture Notes in Computer Science, 2005, Volume 3500/2005, 283-295.