When using the package, please acknowledge your use of TreeDist in the article text, and cite the papers describing the metrics that you employ. For example, "Mutual Phylogenetic Information similarity metrics (Smith 2020a) were calculated using the R package TreeDist v2.9.1 (Smith 2020b)". For tree space mappings, cite Smith (2022).

Smith MR (2020). “Information theoretic Generalized Robinson-Foulds metrics for comparing phylogenetic trees.” Bioinformatics, 36(20), 5007–5013. doi:10.1093/bioinformatics/btaa614.

Smith MR (2022). “Robust analysis of phylogenetic tree space.” Systematic Biology, 71(5), 1255-1270. doi:10.1093/sysbio/syab100.

Smith MR (2020). TreeDist: Distances between Phylogenetic Trees. R package version 2.9.1. doi:10.5281/zenodo.3528124.

Corresponding BibTeX entries:

  @Article{Smith2020,
    doi = {10.1093/bioinformatics/btaa614},
    title = {Information theoretic Generalized Robinson-Foulds metrics
      for comparing phylogenetic trees},
    author = {Martin R. Smith},
    journal = {Bioinformatics},
    volume = {36},
    number = {20},
    pages = {5007–5013},
    year = {2020},
  }

  @Article{Smith2022,
    doi = {10.1093/sysbio/syab100},
    title = {Robust analysis of phylogenetic tree space},
    author = {Martin R. Smith},
    journal = {Systematic Biology},
    volume = {71},
    number = {5},
    pages = {1255-1270},
    year = {2022},
  }

  @Manual{TreeDist,
    title = {TreeDist: Distances between Phylogenetic Trees. R package
      version 2.9.1},
    author = {Martin R. Smith},
    doi = {10.5281/zenodo.3528124},
    journal = {Comprehensive R Archive Network},
    year = {2020},
  }