Introduction | Parsimony reconstructions | Likelihood reconstructions | Fitting for discrete comparative data | Session info | References

Installing R | Installing the phangorn library | Getting started | Set the working directory | Read in the example file datasets: | Viewing the data | Intertwining trees and network functions | 1A: | 1B: | 1C: | Extras... | Figure 4

Introduction | Getting started | Distance based methods | Bootstrap | Parsimony | Branch and bound | Maximum likelihood | Model selection | Conducting a ML tree | Exporting a tree | Molecular dating with a strict clock for ultrametric and tipdated phylogenies | Session info | References

consensusNet | neighborNet | Adding support values | Estimating edge weights (nnls) | Import and export networks, advanced functions for networx objects | Session Information | References

Introduction | List of functions | Getting started | Split Networks | Data Types | Plotting a Split Network: | Plotting Explicit Networks | Summary | Session info | References

Introducción | Lista de funciones | Para empezar | Redes dividida o implicitas | Tipos de datos | Para graficar una Red Dividida | Para graficar una Red Explícita | Resumen | Session info | References

Changes in phangorn 3.0 | Session info | References

Introduction | User defined data formats | Markov models of character evolution | Estimation of non-standard transition rate matrices | Predefined models for user defined data | Codon substitution models | Session info | References

Model comparison | Bootstrap | Generating trees | Session info | References

Load packages | Load data | Parsimony | Branch and bound | Root trees | Plot trees | Consensus tree | Session info | References

apex: Phylogenetic Methods for Multiple Gene Data | Installing apex | Importing data | ape wrappers | phangorn wrappers | New object classes | multidna | multiphyDat | Handling data | Building trees | Distance-based trees | Likelihood-based trees | Exporting data