Premise of the study: Reconstructions of ancestral character states are among
the most widely used analyses for evaluating the morphological, cytological,
or ecological evolution of an organismic lineage. The software application
Mesquite remains the most popular application for such reconstructions among
plant scientists, even though its support for automating complex analyses is
limited. A software tool is needed that automates the reconstruction and
visualization of ancestral character states with Mesquite and similar
applications. Methods and Results: A set of command line–based Python scripts
was developed that (a) communicates standardized input to and output from the
software applications Mesquite, BayesTraits, and TreeGraph2; (b) automates the
process of ancestral character state reconstruction; and (c) facilitates the
visualization of reconstruction results. Conclusions: WARACS provides a simple
tool that streamlines the reconstruction and visualization of ancestral
character states over a wide array of parameters, including tree distribution,
character state, and optimality criterion