Maximum likelihood trees computed from the 100-OTU Graphidaceae dataset with ambiguous regions excluded (left) and recoded using PICS-Ord with Ngila zeta cost scores (right). A GTR-Gamma model was applied to the DNA partition and a GTR model for the PICS-Ord code partition (GTR-CAT for rapid bootstrapping in both cases). Bootstrap support values are indicated next to the branches. Grey triangles indicate major clades with different position in both analyses, and black lines indicate clades with internal topology differing between analyses. Short arrows indicate nodes with increased (black) or decreased (grey) support under PICS-Ord and long arrows indicate nodes present either with ambiguous regions excluded (grey) or under PICS-Ord (black).
Lücking et al. BMC Bioinformatics 2011 12:10 doi:10.1186/1471-2105-12-10