PhyML

PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). (http://packages.ubuntu.com/lucid/science/phyml)


References in zbMATH (referenced in 11 articles )

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  1. Collienne, Lena; Gavryushkin, Alex: Computing nearest neighbour interchange distances between ranked phylogenetic trees (2021)
  2. Klawitter, Jonathan: The agreement distance of unrooted phylogenetic networks (2020)
  3. Monod, Anthea; Kališnik, Sara; Patiño-Galindo, Juan Ángel; Crawford, Lorin: Tropical sufficient statistics for persistent homology (2019)
  4. Warnow, Tandy (ed.): Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret (2019)
  5. Cybis, Gabriela B.; Valk, Marcio; Lopes, Sílvia R. C.: Clustering and classification problems in genetics through (U)-statistics (2018)
  6. Bordewich, Magnus; Linz, Simone; Semple, Charles: Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks (2017)
  7. Sumner, Jeremy G.; Jarvis, Peter D.; Francis, Andrew R.: A representation-theoretic approach to the calculation of evolutionary distance in bacteria (2017)
  8. Jiang, Yu-Shan; Zhang, Dong-Kai; Wang, Xiao-Min; Zhu, Wen-Yan: Exploring high dimension large data correlation analysis with mutual information and application (2016)
  9. Zhu, Sha; Steel, Mike: Does random tree puzzle produce Yule-Harding trees in the many-taxon limit? (2013)
  10. Picardi, Ernesto; Quagliariello, Carla: EdiPy: A resource to simulate the evolution of plant mitochondrial genes under the RNA editing (2006)
  11. Stamatakis, Alexandros; Ludwig, Thomas; Meier, Harald: Parallel inference of a 10.000-taxon phylogeny with maximum likelihood (2004)