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)
Keywords for this software
References in zbMATH (referenced in 4 articles )
Showing results 1 to 4 of 4.
- Bordewich, Magnus; Linz, Simone; Semple, Charles: Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks (2017)
- 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)
- Picardi, Ernesto; Quagliariello, Carla: EdiPy: A resource to simulate the evolution of plant mitochondrial genes under the RNA editing (2006)
- Stamatakis, Alexandros; Ludwig, Thomas; Meier, Harald: Parallel inference of a 10.000-taxon phylogeny with maximum likelihood (2004)