ML sessions data for the 12th International Workshop on Virus Evolution and Molecular Epidemiology, Athens, 2006

    http://www.cibiv.at/~hschmidt/veme/

    Find below the links to the exercises, links to download, and general information and papers.

    The exercises:

    • Advanced Module
      • Maximum likelihood methods in phylogenetics
    • Basic Module
      • Maximum likelihood methods in molecular phylogenetics
      • Tracing phylogenetic signal in datasets

    Papers and Documents:

    • TREE-PUZZLE
      • Application note about TREE-PUZZLE by Schmidt et al.
      • CPBI chapter with a hands-on practical by Schmidt and von Haeseler
      • A good description about phylogenetic problems and how to fix them by Sanderson and Shaffer
      • TREE-PUZZLE Manual
    • IQPNNI
      • IQPNNI paper by Vinh and von Haeseler

    Programs:

    • treepuzzle-clicky.exe and treepuzzle.exe - Windows executables (5.2.pl14, Windows, 32bit)
    • treepuzzle-clicky-macosx.gz and treepuzzle-macosx.gz - Mac OS X executables (5.2.pl14)
    • iqpnni-macosx.gz - Mac OS X executables (IQPNNI 3.0.1)
    • iqpnni.exe - Windows executables (IQPNNI 3.0.1, Windows, 32bit)

    (Note: both TREE-PUZZLE executables are identical except for the name. The latter avoids the window to close if you click-start from a file manager.)
    To re-do the exercise at home, you might want to download the following software onto your computer:
    • TREE-PUZZLE from http://www.tree-puzzle.de
    • IQPNNI from http://www.cibiv.at/software/iqpnni/
    • (Especially for Windows:) Gsview and Ghostscript to view the likelihood mapping diagrams, download from http://www.cs.wisc.edu/~ghost/gsview/. This software can also be used to convert them into PDF.
    • Copy the datasets linked in the exercises!