PhyloNetwork

Perl package Bio::PhyloNetwork: A perl package and an alignment tool for phylogenetic networks. Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene transfer. While most phylogenetics tools implement a wide range of algorithms on phylogenetic trees, there exist only a few applications to work with phylogenetic networks, none of which are open-source libraries, and they do not allow for the comparative analysis of phylogenetic networks by computing distances between them or aligning them. Results: In order to improve this situation, we have developed a Perl package that relies on the BioPerl bundle and implements many algorithms on phylogenetic networks. We have also developed a Java applet that makes use of the aforementioned Perl package and allows the user to make simple experiments with phylogenetic networks without having to develop a program or Perl script by him or herself. Conclusion: The Perl package is available as part of the BioPerl bundle, and can also be downloaded. A web-based application is also available (see availability and requirements). The Perl package includes full documentation of all its features.


References in zbMATH (referenced in 27 articles , 1 standard article )

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  1. Hendriksen, Michael; Francis, Andrew: A partial order and cluster-similarity metric on rooted phylogenetic trees (2020)
  2. Döcker, Janosch; van Iersel, Leo; Kelk, Steven; Linz, Simone: Deciding the existence of a cherry-picking sequence is hard on two trees (2019)
  3. Erdős, Péter L.; Semple, Charles; Steel, Mike: A class of phylogenetic networks reconstructable from ancestral profiles (2019)
  4. Pons, Joan Carles; Semple, Charles; Steel, Mike: Tree-based networks: characterisations, metrics, and support trees (2019)
  5. Gambette, Philippe; Gunawan, Andreas D. M.; Labarre, Anthony; Vialette, Stéphane; Zhang, Louxin: Solving the tree containment problem in linear time for nearly stable phylogenetic networks (2018)
  6. Wicke, Kristina; Fischer, Mareike: Phylogenetic diversity and biodiversity indices on phylogenetic networks (2018)
  7. Gambette, Philippe; Huber, K. T.; Kelk, S.: On the challenge of reconstructing level-1 phylogenetic networks from triplets and clusters (2017)
  8. Gambette, Philippe; van Iersel, Leo; Kelk, Steven; Pardi, Fabio; Scornavacca, Celine: Do branch lengths help to locate a tree in a phylogenetic network? (2016)
  9. Gavryushkin, Alex; Drummond, Alexei J.: The space of ultrametric phylogenetic trees (2016)
  10. Huber, Katharina T.; Moulton, Vincent; Steel, Mike; Wu, Taoyang: Folding and unfolding phylogenetic trees and networks (2016)
  11. Willson, Stephen J.: Comparing and simplifying distinct-cluster phylogenetic networks (2016)
  12. Cordue, Paul; Linz, Simone; Semple, Charles: Phylogenetic networks that display a tree twice (2014)
  13. van Iersel, Leo; Moulton, Vincent: Trinets encode tree-child and level-2 phylogenetic networks (2014)
  14. Bogdanowicz, Damian; Giaro, Krzysztof: On a matching distance between rooted phylogenetic trees (2013)
  15. Huber, K. T.; Moulton, V.: Encoding and constructing 1-nested phylogenetic networks with trinets (2013)
  16. Asano, Tetsuo; Jansson, Jesper; Sadakane, Kunihiko; Uehara, Ryuhei; Valiente, Gabriel: Faster computation of the Robinson-Foulds distance between phylogenetic networks (2012)
  17. Gambette, Philippe; Huber, Katharina T.: On encodings of phylogenetic networks of bounded level (2012)
  18. Arenas, Miguel; Patricio, Mateus; Posada, David; Valiente, Gabriel: Characterization of phylogenetic networks with nettest (2010) ioport
  19. Cardona, Gabriel; Llabrés, Mercè; Rosselló, Francesc; Valiente, Gabriel: Path lengths in tree-child time consistent hybridization networks (2010)
  20. Cardona, Gabriel; Llabrés, Mercè; Rosselló, Francesc; Valiente, Gabriel: Nodal distances for rooted phylogenetic trees (2010)

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