To cite RRphylo implementations and auxilliary functions in
publications use:

RRphylo package, search.shift, and auxilliary functions

  Castiglione, S., Tesone, G., Piccolo, M., Melchionna, M., Mondanaro,
  A., Serio, C., Di Febbraro, M., & Raia, P.(2018). A new method for
  testing evolutionary rate variation and shifts in phenotypic
  evolution. Methods in Ecology and Evolution, 9: 974-983.
  doi:10.1111/2041-210X.12954

A BibTeX entry for LaTeX users is

  @Article{,
    title = {A new method for testing evolutionary rate variation and shifts in phenotypic evolution.},
    author = {{Silvia Castiglione} and {Gianmarco Tesone} and {Martina Piccolo} and {Marina Melchionna} and {Alessandro Mondanaro} and {Carmela Serio} and {Mirko Di Febbraro} and {Pasquale Raia}},
    journal = {Methods in Ecology and Evolution},
    year = {2018},
    volume = {9},
    pages = {974-983},
    url = {https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12954},
  }

multiple regression version of RRphylo

  Serio, C., Castiglione, S., Tesone, G., Piccolo, M., Melchionna, M.,
  Mondanaro, A., Di Febbraro, M., & Raia, P.(2019). Macroevolution of
  toothed whales exceptional relative brain size. Evolutionary Biology,
  46: 332-342. doi:10.1007/s11692-019-09485-7

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Macroevolution of toothed whales exceptional relative brain size.},
    author = {{Carmela Serio} and {Silvia Castiglione} and {Gianmarco Tesone} and {Martina Piccolo} and {Marina Melchionna} and {Alessandro Mondanaro} and {Mirko Di Febbraro} and {Pasquale Raia}},
    journal = {Evolutionary Biology},
    year = {2019},
    volume = {46},
    pages = {332-342},
    url = {https://link.springer.com/article/10.1007/s11692-019-09485-7},
  }

  Melchionna, M., Mondanaro, A., Serio, C., Castiglione, S., Di
  Febbraro, M., Rook, L.,Diniz-Filho,J.A.F., Manzi, G., Profico, A.,
  Sansalone, G., & Raia, P.(2020). Macroevolutionary trends of brain
  mass in Primates. Biological Journal of the Linnean Society, 129:
  14-25 doi:10.1093/biolinnean/blz161

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Macroevolutionary trends of brain mass in Primates.},
    author = {{Marina Melchionna} and {Alessandro Mondanaro} and {Carmela Serio} and {Silvia Castiglione} and {Mirko Di Febbraro} and {Lorenzo Rook} and {José Alexandre Diniz-Filho} and {Giorgio Manzi} and {Antonio Profico} and {Gabriele Sansalone} and {Pasquale Raia}},
    journal = {Biological Journal of the Linnean Society},
    year = {2020},
    volume = {129},
    pages = {14-25},
    url = {https://academic.oup.com/biolinnean/advance-article/doi/10.1093/biolinnean/blz161/5614248},
  }

Ancestral state integration in RRphylo (RRphylo-noder)

  Castiglione, S., Serio, C., Mondanaro, A., Melchionna, M.,
  Carotenuto, F., Di Febbraro, M., Profico, A., Tamagnini, D., & Raia,
  P. (2020). Ancestral State Estimation with Phylogenetic Ridge
  Regression. Evolutionary Biology, 47: 220-232.
  doi:10.1007/s11692-020-09505-x

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Ancestral State Estimation with Phylogenetic Ridge Regression},
    author = {{Silvia Castiglione} and {Carmela Serio} and {Alessandro Mondanaro} and {Marina Melchionna} and {Francesco Carotenuto} and {Mirko Di Febbraro} and {Antonio Profico} and {Davide Tamagnini} and {Pasquale Raia}},
    journal = {Evolutionary Biology},
    year = {2020},
    volume = {47},
    pages = {220-232},
    url = {https://link.springer.com/article/10.1007/s11692-020-09505-x},
  }

search.trend

  Castiglione, S., Serio, C., Mondanaro, A., Di Febbraro, M., Profico,
  A., Girardi, G., & Raia, P.(2019). Simultaneous detection of
  macroevolutionary patterns in phenotypic means and rate of change
  with and within phylogenetic trees including extinct species. PLoS
  ONE, 14: e0210101. doi.org/10.1371/journal.pone.0210101

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Simultaneous detection of macroevolutionary patterns in phenotypic means and rate of change                          with and within phylogenetic trees including extinct species.},
    author = {{Silvia Castiglione} and {Carmela Serio} and {Alessandro Mondanaro} and {Mirko Di Febbraro} and {Antponio Profico} and {Giorgia Girardi} and {Pasquale Raia}},
    journal = {PLoS ONE},
    year = {2019},
    volume = {14},
    pages = {e0210101},
    url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0210101},
  }

search.conv

  Castiglione, S., Serio, C., Tamagnini, D., Melchionna, M., Mondanaro,
  A., Di Febbraro, M., Profico, A., Piras, P.,Barattolo, F., & Raia, P.
  (2019). A new, fast method to search for morphological convergence
  with shape data. PLoS ONE, 14, e0226949.
  doi:10.1371/journal.pone.0226949

A BibTeX entry for LaTeX users is

  @Article{,
    title = {A new, fast method to search for morphological convergence with shape data.},
    author = {{Silvia Castiglione} and {Carmela Serio} and {Davide Tamagnini} and {Marina Melchionna} and {Alessandro Mondanaro} and {Mirko Di Febbraro} and {Antonio Profico} and {Paolo Piras} and {Filippo Barattolo} and {Pasquale Raia}},
    journal = {PLoS ONE},
    year = {2019},
    volume = {14},
    pages = {e0226949},
    url = {https://doi.org/10.1371/journal.pone.0226949},
  }

fix.poly

  Castiglione, S., Serio, C., Piccolo, M., Mondanaro, A., Melchionna,
  M., Di Febbraro, M., Sansalone, G., Wroe, S., & Raia, P. (2020). The
  influence of domestication, insularity and sociality on the tempo and
  mode of brain size evolution in mammals. Biological Journal of the
  Linnean Society, 132, 221-231. doi:10.1093/biolinnean/blaa186

A BibTeX entry for LaTeX users is

  @Article{,
    title = {The influence of domestication, insularity and sociality on the tempo and mode of brain size evolution in mammals.},
    author = {{Silvia Castiglione} and {Carmela Serio} and {Martina Piccolo} and {Alessandro Mondanaro} and {Marina Melchionna} and {Mirko Di Febbraro} and {Gabriele Sansalone} and {Stephen Wroe} and {Pasquale Raia}},
    journal = {Biological Journal of the Linnean Society},
    year = {2020},
    volume = {132},
    pages = {221-231},
    url = {https://doi.org/10.1093/biolinnean/blaa186},
  }

conv.map

  Melchionna, M., Profico, A., Castiglione, S., Serio, C., Mondanaro,
  A., Modafferi, M., Tamagnini, D., Maiorano, L. , Raia, P., Witmer,
  L.M., Wroe, S., & Sansalone, G. (2021). A method for mapping
  morphological convergence on three-dimensional digital models: the
  case of the mammalian sabre‐tooth. Palaeontology, 64, 573–584.
  doi:10.1111/pala.12542

A BibTeX entry for LaTeX users is

  @Article{,
    title = {A method for mapping morphological convergence on three-dimensional digital models: the case of the mammalian sabre-tooth},
    author = {{Marina Melchionna} and {Antonio Profico} and {Silvia Castiglione} and {Carmela Serio} and {Alessandro Mondanaro} and {Maria Modafferi} and {Davide Tamagnini} and {Luigi Maiorano} and {Pasquale Raia} and {Lawrence M. Witmer} and {Stephen Wroe} and {Gabriele Sansalone}},
    journal = {Palaeontology},
    year = {2021},
    volume = {64},
    pages = {573–584},
    url = {https://onlinelibrary.wiley.com/doi/10.1111/pala.12542},
  }

rate.map

  Castiglione, S., Melchionna, M., Profico, A., Sansalone, G.,
  Modafferi, M., Mondanaro, A., Wroe, S., Piras, P., & Raia, P. (2021).
  Human face-off: a new method for mapping evolutionary rates on
  three-dimensional digital models. Palaeontology, 65, e12582.
  doi:10.1111/pala.12582

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Human face-off: a new method for mapping evolutionary rates on three-dimensional digital models},
    author = {{Silvia Castiglione} and {Marina Melchionna} and {Antonio Profico} and {Gabriele Sansalone} and {Maria Modafferi} and {Alessandro Mondanaro} and {Stephen Wroe} and {Paolo Piras} and {Pasquale Raia}},
    journal = {Palaeontology},
    year = {2021},
    volume = {65},
    pages = {e12582},
    url = {https://onlinelibrary.wiley.com/doi/10.1111/pala.12582},
  }

tree.merger

  Castiglione, S., Serio, C., Mondanaro, A., Melchionna, M., & Raia,
  P.(2022). Fast Production of Large, Time-Calibrated Informal
  Supertrees with tree.merger. Palaeontology, 65, e12588.
  doi:10.1111/pala.12588

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Fast Production of Large, Time-Calibrated Informal Supertrees with tree.merger},
    author = {{Silvia Castiglione} and {Carmela Serio} and {Alessandro Mondanaro} and {Marina Melchionna} and {Pasquale Raia}},
    journal = {Palaeontology},
    year = {2022},
    volume = {65},
    pages = {e12588},
    url = {https://onlinelibrary.wiley.com/doi/10.1111/pala.12588},
  }