Below you can find a list of functions that facilitate phylogenetic analyses with R:
Download HEIBL. The package contains a collection of function for phylogenetic labwork and data analyses and is best thought of a add-on package to ape.
Reading and writing NEXUS, PHYLIP, and FASTA files containing DNA sequences, discrete or continuous trait data, and distance matrices
Handling of alignments (functions)
Matrix representation with parsimony for supertree construction (functions)
Selection of DNA substitution models (using code of Emmanuel Paradis) (function)
RAxML wrapper (R code)
GARLI wrapper (R code)
MrBayes wrapper (R code)
Multidivtime pipe (details)
Rotating sister clades in a phylogram (function)
Conversion of geographic coordinates from decimal to degree and vive versa (function)
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