PAML

Phylogenetic Analysis by Maximum Likelihood (PAML). PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.


References in zbMATH (referenced in 11 articles )

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  1. Chi, Peter B.; Chattopadhyay, Sujay; Lemey, Philippe; Sokurenko, Evgeni V.; Minin, Vladimir N.: Synonymous and nonsynonymous distances help untangle convergent evolution and recombination (2015)
  2. Ahn, Insung; Son, Hyeon Seok: Computational model for analyzing the evolutionary patterns of the neuraminidase gene of influenza A/H1N1 (2012)
  3. Carmel, Liran; Wolf, Yuri I.; Rogozin, Igor B.; Koonin, Eugene V.: EREM: parameter estimation and ancestral reconstruction by expectation-maximization algorithm for a probabilistic model of genomic binary characters evolution (2010) ioport
  4. de Oliveira Martins, Leonardo; Kishino, Hirohisa: Distribution of distances between topologies and its effect on detection of phylogenetic recombination (2010)
  5. Fan, Xiaodan; Yuan, Yuan; Liu, Jun S.: The EM algorithm and the rise of computational biology (2010)
  6. Nakajima, Yoshihiro; Sato, Mitsuhisa; Aida, Yoshiaki; Boku, Taisuke; Cappello, Franck: Integrating computing resources on multiple grid-enabled job scheduling systems through a grid RPC system (2007) ioport
  7. Xia, Xuhua: Bioinformatics and the cell. Modern computational approaches in genomics, proteomics and transcriptomics (2007)
  8. Picardi, Ernesto; Quagliariello, Carla: EdiPy: A resource to simulate the evolution of plant mitochondrial genes under the RNA editing (2006)
  9. Conery, John S.; Catchen, Julian M.; Lynch, Michael: Model driven service composition (2005) ioport
  10. Pupko, T.; Graur, D.: Fast computation of maximum likelihood trees by numerical approximation of amino acid replacement probabilities (2002)
  11. Yang, Z.: PAML: a program package for phylogenetic analysis by maximum likelihood. (1997) ioport