Citations

If you use the TICR pipeline, PhyloNetworks and SNaQ for your work, please cite the following references.

TICR pipeline

Stenz et al (2015). Exploring tree-like and non-tree-like patterns using genome sequences: An example using the inbreeding plant species Arabidopsis thaliana (L.) Heynh. Systematic Biology, 64(5):809-823

@article{stenz2015exploring,
  title={Exploring tree-like and non-tree-like patterns using genome sequences: an example using the inbreeding plant species Arabidopsis thaliana (L.) Heynh},
  author={Stenz, Noah WM and Larget, Bret and Baum, David A and An{\'e}, C{\'e}cile},
  journal={Systematic Biology},
  volume={64},
  number={5},
  pages={809--823},
  year={2015},
  publisher={Oxford University Press}
}

Ronquist, F., et al. (2012) “MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.” Systematic biology 61.3: 539-542.

@article{ronquist2012mrbayes,
  title={MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space},
  author={Ronquist, Fredrik and Teslenko, Maxim and Van Der Mark, Paul and Ayres, Daniel L and Darling, Aaron and H{\"o}hna, Sebastian and Larget, Bret and Liu, Liang and Suchard, Marc A and Huelsenbeck, John P},
  journal={Systematic biology},
  volume={61},
  number={3},
  pages={539--542},
  year={2012},
  publisher={Oxford University Press}
}

Larget, B., et al (2010). “BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis.” Bioinformatics 26.22: 2910-2911.

@article{larget2010bucky,
  title={BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis},
  author={Larget, Bret R and Kotha, Satish K and Dewey, Colin N and An{\'e}, C{\'e}cile},
  journal={Bioinformatics},
  volume={26},
  number={22},
  pages={2910--2911},
  year={2010},
  publisher={Oxford University Press}
}

Snir, S., and Satish R. (2012). “Quartet MaxCut: a fast algorithm for amalgamating quartet trees.” Molecular phylogenetics and evolution 62.1: 1-8.

@article{snir2012quartet,
  title={Quartet MaxCut: a fast algorithm for amalgamating quartet trees},
  author={Snir, Sagi and Rao, Satish},
  journal={Molecular phylogenetics and evolution},
  volume={62},
  number={1},
  pages={1--8},
  year={2012},
  publisher={Elsevier}
}

PhyloNetworks for network estimation (SNaQ)

Solís-Lemus, C., P. Bastide, and C. Ané. (2017) “PhyloNetworks: a package for phylogenetic networks.” Molecular biology and evolution 34.12: 3292-3298.

@article{solis2017phylonetworks,
  title={PhyloNetworks: a package for phylogenetic networks},
  author={Sol{\'\i}s-Lemus, Claudia and Bastide, Paul and An{\'e}, C{\'e}cile},
  journal={Molecular biology and evolution},
  volume={34},
  number={12},
  pages={3292--3298},
  year={2017},
  publisher={Oxford University Press}
}

Solís-Lemus, C., and C. Ané. (2016) “Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting.” PLoS genetics 12.3: e1005896.

@article{solis2016inferring,
  title={Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting},
  author={Sol{\'\i}s-Lemus, Claudia and An{\'e}, C{\'e}cile},
  journal={PLoS genetics},
  volume={12},
  number={3},
  pages={e1005896},
  year={2016},
  publisher={Public Library of Science San Francisco, CA USA}
}

PhyloNetworks for trait models

Solís-Lemus, C., P. Bastide, and C. Ané. (2017) “PhyloNetworks: a package for phylogenetic networks.” Molecular biology and evolution 34.12: 3292-3298.

@article{solis2017phylonetworks,
  title={PhyloNetworks: a package for phylogenetic networks},
  author={Sol{\'\i}s-Lemus, Claudia and Bastide, Paul and An{\'e}, C{\'e}cile},
  journal={Molecular biology and evolution},
  volume={34},
  number={12},
  pages={3292--3298},
  year={2017},
  publisher={Oxford University Press}
}

Continuous traits

Bastide, Paul, et al. (2018) “Phylogenetic comparative methods on phylogenetic networks with reticulations.” Systematic biology 67.5: 800-820.

@article{bastide2018phylogenetic,
  title={Phylogenetic comparative methods on phylogenetic networks with reticulations},
  author={Bastide, Paul and Sol{\'\i}s-Lemus, Claudia and Kriebel, Ricardo and William Sparks, K and An{\'e}, C{\'e}cile},
  journal={Systematic biology},
  volume={67},
  number={5},
  pages={800--820},
  year={2018},
  publisher={Oxford University Press}
}

Discrete traits

Solís-Lemus, C., P. Bastide, and C. Ané. (2017) “PhyloNetworks: a package for phylogenetic networks.” Molecular biology and evolution 34.12: 3292-3298.

@article{solis2017phylonetworks,
  title={PhyloNetworks: a package for phylogenetic networks},
  author={Sol{\'\i}s-Lemus, Claudia and Bastide, Paul and An{\'e}, C{\'e}cile},
  journal={Molecular biology and evolution},
  volume={34},
  number={12},
  pages={3292--3298},
  year={2017},
  publisher={Oxford University Press}
}

Karimi, Nisa, et al. (2020). “Reticulate evolution helps explain apparent homoplasy in floral biology and pollination in baobabs (Adansonia; Bombacoideae; Malvaceae).” Systematic Biology 69.3: 462-478.

@article{karimi2020reticulate,
  title={Reticulate evolution helps explain apparent homoplasy in floral biology and pollination in baobabs (Adansonia; Bombacoideae; Malvaceae)},
  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},
  journal={Systematic Biology},
  volume={69},
  number={3},
  pages={462--478},
  year={2020},
  publisher={Oxford University Press}
}

Baobabs data

@article{karimi2020reticulate,
  title={Reticulate evolution helps explain apparent homoplasy in floral biology and pollination in baobabs (Adansonia; Bombacoideae; Malvaceae)},
  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},
  journal={Systematic Biology},
  volume={69},
  number={3},
  pages={462--478},
  year={2020},
  publisher={Oxford University Press}
}