CITATION.bib

% reference for the software itself
@article{2017SolislemusBastideAne_PhyloNetworks,
  author = {Sol{\'\i}s-Lemus, Claudia and Bastide, Paul and An{\'e}, C{\'e}cile},
  title = {PhyloNetworks: A Package for Phylogenetic Networks},
  journal = {Molecular Biology and Evolution},
  year = {2017},
  volume = {34},
  number = {12},
  pages = {3292-3298},
  doi = {10.1093/molbev/msx235},
}
% paper describing network calibration, based on genetic distances estimated from gene trees
@article{2020Karimi_baobab_discretetraitevolution,
  author = {Karimi, Nisa and Grover, Corrinne E and Gallagher, Joseph P and Wendel, Jonathan F and An{\'e}, C{\'e}cile and Baum, David A},
  title = {Reticulate Evolution Helps Explain Apparent Homoplasy in Floral Biology and Pollination in Baobabs (\textit{{Adansonia}}; {Bombacoideae}; {Malvaceae})},
  journal = {Systematic Biology},
  year = {2020},
  volume = {69},
  number = {3},
  pages = {462-478},
  doi = {10.1093/sysbio/syz073},
}
% dissertation describing semidirected NNI (nearest neighbor interchange)
% to modify a semidirected network: in Chapter 4
@phdthesis{2020AllenSavietta-Ane,
  author  = {Allen-Savietta, Cora},
  title   = {Estimating Phylogenetic Networks from Concatenated Sequence Alignments},
  school  = {The University of Wisconsin - Madison},
  year    = 2020,
  note = {Ph.D. dissertation, advised by Cécile Ané, ProQuest Dissertations & Theses 28263540},
  url = {https://www.proquest.com/docview/2476856270/},
  pages = 165,
}