QNet

QNet: a software package for estimating phylogenetic networks based on quartets. QNet is a software package written in Java which encompasses methods for generating phylogenetic networks from quartet data, as per the method described in [1]. The method takes as input the set of all quartet tree topologies for a given data set, together with a branch length for each topology. These branch lengths must be precomputed by the user. Included in the package are two simple applications for generating quartet weight data. GWeight utilizes statistical geometry [2] to generate quartet weights. LengthWeighter is a front-end for the Tree-Puzzle software [3] for generating likelihood quartet weights. Using the quartet data, QNet employs an agglomerative approach to construct a planar split network, that summarises the relations described by the quartets.The resulting networks are output in Nexus format for easy visualization using the SplitsTree software package [4]. The Filterer application may be used to reduce the complexity of networks for ease of visualizing and interpretation of results.


References in zbMATH (referenced in 11 articles )

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  1. Poormohammadi, Hadi; Zarchi, Mohsen Sardari; Ghaneai, Hossein: NCHB: a method for constructing rooted phylogenetic networks from rooted triplets based on height function and binarization (2020)
  2. Huber, Katharina T.; Moulton, Vincent; Semple, Charles; Wu, Taoyang: Quarnet inference rules for level-1 networks (2018)
  3. Prohaska, Sonja J.; Berkemer, Sarah J.; Gärtner, Fabian; Gatter, Thomas; Retzlaff, Nancy; Höner zu Siederdissen, Christian; Stadler, Peter F.: Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem (2018)
  4. Balvočiūtė, Monika; Bryant, David; Spillner, Andreas: When can splits be drawn in the plane? (2017)
  5. Asano, Tetsuo; Jansson, Jesper; Sadakane, Kunihiko; Uehara, Ryuhei; Valiente, Gabriel: Faster computation of the Robinson-Foulds distance between phylogenetic networks (2012)
  6. Eslahchi, Changiz; Hassanzadeh, Reza; Mottaghi, Ehsan; Habibi, Mahnaz; Pezeshk, Hamid; Sadeghi, Mehdi: Constructing circular phylogenetic networks from weighted quartets using simulated annealing (2012)
  7. Calders, Toon; Ramon, Jan; Van Dyck, Dries: All normalized anti-monotonic overlap graph measures are bounded (2011)
  8. Grünewald, S.; Koolen, J. H.; Lee, W. S.: Quartets in maximal weakly compatible split systems (2009)
  9. Grünewald, S.; Moulton, V.; Spillner, A.: Consistency of the QNet algorithm for generating planar split networks from weighted quartets (2009)
  10. Grünewald, Stefan; Huber, Katharina T.; Moulton, Vincent; Semple, Charles; Spillner, Andreas: Characterizing weak compatibility in terms of weighted quartets (2009)
  11. Grünewald, S.; Huber, K. T.; Wu, Q.: Two novel closure rules for constructing phylogenetic super-networks (2008)