Search for phylogenetic trees that are optimal using a user-defined criterion.

“TreeSearch” is an R package that contains a “shiny” user interface for interactive tree search and exploration of results, including character visualization, rogue taxon detection, tree space mapping, and cluster consensus trees.

It handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith (2019) using the “Morphy” C library (Brazeau et al. 2017), and implements implied weighting (Goloboff, 1993), Profile Parsimony (Faith and Trueman, 2001) and Successive Approximations (Farris, 1969). Custom optimality criteria and search approaches can be defined.

Installation

Full installation instructions, including notes on installing R, are available in a vignette.

Install and load the stable version from CRAN as follows:

Some features available through the GUI require versions of packages scheduled for release to CRAN in late 2021. Until then, you can install them using:

if(!require("remotes")) install.packages("remotes")
if (packageVersion("ape" < "5.5.2")) 
  remotes::install_github("emmanuelparadis/ape")
if (packageVersion("TreeTools") < "1.5.0.9100")
  remotes::install_github("ms609/TreeTools")

Install the development version of “TreeSearch” with:

remotes::install_github('ms609/TreeSearch')
library("TreeSearch")

Quick start

Launch a graphical user interface (development version only) by typing TreeSearch::EasyTrees() in the R console.

For more control over search settings, see ?MaximizeParsimony().

Documentation

Please note that the ‘TreeSearch’ project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

References

Brazeau M. D., Smith M. R., Guillerme T. (2017). MorphyLib: a library for phylogenetic analysis of categorical trait data with inapplicability. doi: 10.5281/zenodo.815372.

Brazeau, M. D., Guillerme, T. and Smith, M. R. (2019). An algorithm for morphological phylogenetic analysis with inapplicable data. Systematic Biology, 68(4), 619-631. doi: 10.1093/sysbio/syy083.

Faith D. P., Trueman J. W. H. (2001). Towards an inclusive philosophy for phylogenetic inference. Systematic Biology, 50(3), 331–350. doi: 10.1080/10635150118627.

Farris, J. S. (1969). A successive approximations approach to character weighting. Systematic Biology, 18(4), 374–385. doi: 10.2307/2412182.

Goloboff, P. A. (1993). Estimating character weights during tree search. Cladistics, 9(1), 83–91. doi: 10.1111/j.1096-0031.1993.tb00209.x.

Goloboff, P. A., Torres, A., Arias, J. S. (2018). Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology. Cladistics, 34(4), 407–437. doi: 10.1111/cla.12205.