The Robinson–Foulds distance | Information-corrected Robinson–Foulds distance | Generalized Robinson–Foulds distances | Constructing a matching | What next? | References

Introduction | Models of trait evolution | Brownian motion | Pagel's lambda | Delta | Kappa | Ornstein-Uhlenbeck | ACDC and Early Burst | psi and multispi | Estimate Pagel's lambda alongside other modes | Rate heterogeneous models of evolution | rate heterogeneity selected a priori | rate heterogeneity with no a priori information | timeSlice model | modeSlice model | Nested models of evolution | Bayesian estimation of tree transformation models | Character displacement models | Fast estimation of Phylogenetic Generalised Least Squares

Loading trees | Calculating distances | Pairs of trees | Multiple comparisons | Pairwise comparison | Trees with different tip labels | Other calculations | What next?

Partition distances | Quartet distances | Normalization | Asymmetric differences | Quartet similarity in a pair of random trees | Independence | Minimum quartet similarity | References

Shiny app | Scripting at the R command line | Comparing trees' dispersal / hypervolume | Distances from median | Consensus resolution | References

Normalizing | Nye et al. tree similarity | Normalizing to random similarity | Testing similarity to a known tree | Example | What next? | References

References

Loading trees | Calculating distances | Pairs of trees | Multiple comparisons | Visualizing a matching | What next?

Tree space analysis via user interface | Avoiding common pitfalls in tree space analysis | Using a suitable distance metric | Mapping distances | Identifying clusters | Identifying islands | Validating a mapping | Comparing cluster size | Self-organizing maps | What next? | References

Getting started | Command line tree search | Evaluating clade support | Exploring taxon stability | Implied weighting | Constraining a search | Where next? | References

Using custom optimality criteria | Maximizing tree balance | Maximizing tree distance | Searching using implied weights | What next? | References

Loading trees into the GUI | Exploring the consensus | The structure of tree space | Tree space analysis in R | Generate distances | Identify clustering structure | Mapping tree space | Using tree clustering to understand tree space structure | Where next? | References

Getting started | Scoring a tree, and conducting a tree search | View the results | Where next? | References

Load raw data | From an Excel spreadsheet | From a text or CSV (comma separated values) file | From a Nexus file | From a TNT file | Processing raw data | Store processed data | What next? | References

Create a blank plot | Plot two stylised plots side by side, and plot data | Styling points | Cartesian coordinates | Contours | Magnification | Further tutorials | Bugs and feature requests

Installation | Simple installation | For advanced users | What next?

What next?

Your own data | Customization | References

Interpolation within a sampled region | Where next

Your own data | Where next

Shared phylogenetic information | Conflicting splits can nevertheless be instructive | Mutual clustering information | Nye et al. tree similarity metric | Jaccard–Robinson–Foulds metric | Matching Split Distance | Information theoretic alternative | References

Bayesian analysis | Parsimony analysis | Analysing output data | References

Summary | Trees 1--10 | Trees 11--20 | Trees 21--30 | Trees 31--40 | Trees 41--50 | Trees 51--60 | Trees 61--70 | Trees 71--80 | Trees 81--90 | Trees 91--100 | References

Where next

Set up | Select trees to analyse | Initial appraisal | Detect rogue taxa | Visualize results | References

Scope of this document | A philosophy of parsimony | Application of Occam's Razor | An information theoretic basis | Implementation | Where next | References

Manual entry | From a file | Nexus files | Newick files | Trees from TNT | Other formats | Export (write) trees | What next?

Splits | Quantifying information | Application to splits | Entropy | References

Loading trees | Calculating distances | Comparing multiple trees | Citation

Summary | Trees 1--10 | Trees 11--20 | Trees 21--30 | Trees 31--40 | Trees 41--50 | Trees 51--60 | Trees 61--70 | Trees 71--80 | Trees 81--90 | Trees 91--100 | References