Inapplicable data in morphological phylogenetics

Martin R. Smith


TreeSearch is an R package that allows, among other things, parsimony search on morphological datasets that contain inapplicable data, following the algorithm proposed by Brazeau, Guillerme and Smith (2017).

In brief, this algorithm modifies the Fitch algorithm to count the total number of homoplasious events on a tree.

Getting started

A companion vignette gives details on installing the package and getting up and running.

Once installed, load the inapplicable package into R using


Implied weighting

Equal weights produces trees that are less accurate and less precise than implied weights (Smith, 2017); equally weighted analysis should never be conducted without also considering the results of implied weights (Goloboff, 1997), ideally under a range of concavity constants (cf. Smith & Ortega-Hernández, 2014).

The simplest way to conduct an implied weights search is to use the functions


which operate in the same fashion as their equally-weighted counterparts, with the option of specifying a concavity constant (k) using the parameter concavity=k (default = 4).


Brazeau, M. D., Guillerme, T., & Smith, M. R. (2017). Morphological phylogenetic analysis with inapplicable data. Biorxiv. doi:10.1101/209775

Goloboff, P. A. (1997). Self-weighted optimization: tree searches and character state reconstructions under implied transformation costs. Cladistics, 13(3), 225–245. Retrieved from

Nixon, K. C. (1999). The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics, 15(4), 407–414. doi:10.1111/j.1096-0031.1999.tb00277.x

Smith, M. R. (2017). Quantifying and visualising divergence between pairs of phylogenetic trees. BioRxiv. doi:10.1101/227942

Smith, M. R., & Ortega-Hernández, J. (2014). Hallucigenia’s onychophoran-like claws and the case for Tactopoda. Nature, 514(7522), 363–366. doi:10.1038/nature13576

Vinther, J., Van Roy, P., & Briggs, D. E. G. (2008). Machaeridians are Palaeozoic armoured annelids. Nature, 451(7175), 185–188. doi:10.1038/nature06474