phytools - Phylogenetic Tools for Comparative Biology (and Other Things)
A wide range of methods for phylogenetic analysis -
concentrated in phylogenetic comparative biology, but also
including numerous techniques for visualizing, analyzing,
manipulating, reading or writing, and even inferring
phylogenetic trees. Included among the functions in
phylogenetic comparative biology are various for ancestral
state reconstruction, model-fitting, and simulation of
phylogenies and trait data. A broad range of plotting methods
for phylogenies and comparative data include (but are not
restricted to) methods for mapping trait evolution on trees,
for projecting trees into phenotype space or a onto a
geographic map, and for visualizing correlated speciation
between trees. Lastly, numerous functions are designed for
reading, writing, analyzing, inferring, simulating, and
manipulating phylogenetic trees and comparative data. For
instance, there are functions for computing consensus
phylogenies from a set, for simulating phylogenetic trees and
data under a range of models, for randomly or non-randomly
attaching species or clades to a tree, as well as for a wide
range of other manipulations and analyses that phylogenetic
biologists might find useful in their research.
