Package: MonoPhy 1.3.2

1 Introduction | 2 Installation | 2.1 CRAN | 2.2 Development Version from GitHub | 3 Use | 3.1 Load Data | 3.1.1 Example Files | 3.1.2 Own Files | 3.2 Run Main Analysis | 3.2.1 Taxonomy Based on Tip Labels | 3.2.2 Taxonomy Based on File | 3.2.3 Taxonomy Downloaded from Web | 3.2.4 Other Options | 3.3 Accessing the Results | 3.3.1 First Impression - Summary and Results Tables | 3.3.2 Further Look - Customized Access to Detailed Results | 3.4 Plotting | 3.4.1 Monophyly Plot | 3.4.2 Taxonomy Plot | 3.4.3 Monophyly-Taxonomy Mirror Plot | 3.4.4 Intruder Plot | 3.4.5 Solutions for Large Trees | 4 Final Notes