“TreeSearch” (Smith 2021) is an R package that contains a “shiny” user interface for interactive tree search and exploration of results, including character visualization, rogue taxon detection (Smith 2022a), tree space mapping (Smith 2022b), and cluster consensus trees.

Inapplicable character states are handled using the algorithm of Brazeau, Guillerme and Smith (2019) using the “Morphy” C library (Brazeau et al. 2017). Implied weighting (Goloboff, 1993), Profile Parsimony (Faith and Trueman, 2001) and Successive Approximations (Farris, 1969) are implemented; custom optimality criteria and search approaches can also 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:

Install and load the development version of “TreeSearch” with:

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

Errors reading trees

Some users are reporting an error when loading trees from Nexus files: Error in [<-.multiPhylo: argument "..1" is missing, with no default

This arises due to an underlying issue in the “ape” package, which can be fixed by installing a patch:

remotes::install_github("ms609/ape@patch-3")

(You may first need to exit and re-launch R to be sure that the “ape” package is not in use.)

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.

Smith, M. R. (2021). TreeSearch: morphological phylogenetic analysis in R. BioRχiv. doi: 10.1101/2021.11.08.467735.

Smith, M. R. (2022a). Using information theory to detect rogue taxa and improve phylogenetic trees. Systematic Biology, syab099. doi: 10.1093/sysbio/syab099

Smith, M. R. (2022b). Robust analysis of phylogenetic tree space. Systematic Biology, syab100. doi: 10.1093/sysbio/syab100