Please acknowledge your use of TreeSearch and MorphyLib in any article in which they are used, and cite Smith (2021) and Brazeau et al. (2019). For example, 'Phylogenetic search was performed using the R package TreeSearch v1.1.2 (Smith 2021), which uses MorphyLib (Brazeau et al. 2017) to handle inapplicable data (Brazeau et al. 2019)'. The GUI lists recommended citations for methods it employs.

Brazeau MD, Smith MR, Guillerme T (2017). MorphyLib: a library for phylogenetic analysis of categorical trait data with inapplicability. Version 0.0.1-alpha.

Brazeau MD, Guillerme T, Smith MR (2019). “An algorithm for morphological phylogenetic analysis with inapplicable data.” Systematic Biology, 64, 619-631.

Smith MR (2018). TreeSearch: phylogenetic tree search using custom optimality criteria. doi:10.5281/zenodo.1042590, R package version 1.1.2.

Smith (2021). TreeSearch: morphological phylogenetic analysis in R. preprint at bioRxiv.<doi:10.1101/2021.11.08.467735>

Corresponding BibTeX entries:

  @Manual{Brazeau2017,
    title = {MorphyLib: a library for phylogenetic analysis of
      categorical trait data with inapplicability},
    author = {Martin D. Brazeau and Martin R. Smith and Thomas
      Guillerme},
    year = {2017},
    note = {Version 0.0.1-alpha},
  }
  @Article{Brazeau2019,
    title = {An algorithm for morphological phylogenetic analysis with
      inapplicable data},
    author = {Martin D. Brazeau and Thomas Guillerme and Martin R.
      Smith},
    journal = {Systematic Biology},
    volume = {64},
    issue = {4},
    pages = {619-631},
    year = {2019},
  }
  @Manual{Smith2018,
    title = {{TreeSearch}: phylogenetic tree search using custom
      optimality criteria},
    author = {Martin R. Smith},
    note = {R package version 1.1.2},
    year = {2018},
    doi = {10.5281/zenodo.1042590},
  }
  @Article{Smith2021,
    title = {{TreeSearch}: morphological phylogenetic analysis in
      {{R}}},
    author = {Martin R. Smith},
    year = {2021},
    journal = {bioR$\chi$iv},
    doi = {10.1101/2021.11.08.467735},
  }