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

Installing treespace | Content overview | Exploring trees with treespace | Identifying clusters of trees | treespaceServer: a web application for treespace | Finding median trees | Emphasising the placement of certain tips or clades | Method: characterising a tree by a vector | References | Authors / Contributors

What does it do? | Fitting a gamma distribution to delay data | Converting a growth rate (r) to a reproduction number (R0) | Standardising labels | Anonymising data

Description | Example

Main features | Example usage | Setup | A succesful model fit | Example of failed model fitting | Multiple models

Overview | Confidence interval | Prediction interval | Comparison to a bootstrap approach | setup | Example 1 - Poisson | Example 2 - Quassipoisson

Examples | Comparing three simple trees | Comparing many trees using an MDS plot | Median trees

Loading treespace and data: | Creating neighbour-joining and maximum likelihood trees: | Using treespace to compare trees | treespace analysis | Using treespace to analyse the BEAST trees in more detail: | References

Related tree distance | Concordance