Performing calibrations using bayclumpr | Reconstructing temperatures in bayclumpr | Including a co-variate (with sample-specific errors in the covariate) | Including a co-variate (without error in the covariate) | Outlook

General acknowledgements

Table of Contents | Working with non-animal nor plant groups in phruta | Creating taxonomic constraints in phruta | ingroup + outgroup | Particular clades | Running PartitionFinder in phruta | Partitioned analyses in RAxML | Identifying rogue taxa

Future directions for phruta

Table of Contents | phruta en Español | What is phruta? | Functions in phruta

Table of Contents | Installing RAxML | Installing PATHd-8 and treePL | Phylogenetic inference with phruta and RAxML | Tree dating in phruta

Table of Contents | To export or not export from phruta | From taxonomic names to sequence alignments, exporting data

Table of Contents | Desde nombres taxonomicos a alineamientos | Guardando objetos intermedios

Table of Contents | Intro tutorial: Clade names to sequence alignments | Saving intermediate files

Additional functions for manipulating data

Manipulando Datos

Manipulating Data | Coindexing | Running functions on treedata.table objects | Dropping and extracting taxa from treedata.table objects

Partially matching trait data and tree(s)

Working with multiphylo objects