# Inapplicable data in a parsimony setting

This document provides a detailed explanation of the algorithm for handling inapplicable data proposed by Brazeau et al. (2017).

We first discuss how the Fitch algorithm works and introduce the problems that it encounters in the face of inapplicable character states.

We then introduce our solution, a new algorithm, implemented in various software packages, and discuss its implications for the coding of characters and ambiguity.

We close with some example trees that demonstrate how our algorithm behaves in more complicated cases.

### References

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