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 43 articles )

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  1. Rodríguez-Horta, Edwin; Lage-Castellanos, Alejandro; Mulet, Roberto: Ancestral sequence reconstruction for co-evolutionary models (2022)
  2. Andres Veidenberg, Ari L: Pline: automatic generation of modern web interfaces for command-line programs (2020) arXiv
  3. Ostash, Bohdan; Anisimova, Maria: Visualizing codon usage within and across genomes: concepts and tools (2020)
  4. Shore, Julia A.; Sumner, Jeremy G.; Holland, Barbara R.: The impracticalities of multiplicatively-closed codon models: a retreat to linear alternatives (2020)
  5. Tahir, Daniah; Glémin, Sylvain; Lascoux, Martin; Kaj, Ingemar: Modeling a trait-dependent diversification process coupled with molecular evolution on a random species tree (2019)
  6. Yoshida, Ruriko; Fukumizu, Kenji; Vogiatzis, Chrysafis: Multilocus phylogenetic analysis with gene tree clustering (2019)
  7. Liu, Yong; Chen, Jingan; Qian, Jieying; Lin, Hao; Sun, Ning; Huang, Zunnan: Evolutionary analysis and structural characterization of \textitAquilariasinensis sesquiterpene synthase in agarwood formation: a computational study (2018)
  8. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  9. Chi, Peter B.; Chattopadhyay, Sujay; Lemey, Philippe; Sokurenko, Evgeni V.; Minin, Vladimir N.: Synonymous and nonsynonymous distances help untangle convergent evolution and recombination (2015)
  10. Erciyes, K.: Distributed and sequential algorithms for bioinformatics (2015)
  11. Soares, André E. R.; Schrago, Carlos G.: The influence of taxon sampling on Bayesian divergence time inference under scenarios of rate heterogeneity among lineages (2015)
  12. Loza-Reyes, E.; Hurn, M. A.; Robinson, A.: Classification of molecular sequence data using Bayesian phylogenetic mixture models (2014)
  13. Schrago, Carlos G.: The limiting distribution of the effective population size of the ancestor of humans and chimpanzees (2014)
  14. Benger, Etam; Sella, Guy: Modeling the effect of changing selective pressures on polymorphism and divergence (2013)
  15. Lafond, Manuel; Swenson, Krister M.; El-Mabrouk, Nadia: Error detection and correction of gene trees (2013)
  16. Ahn, Insung; Son, Hyeon Seok: Computational model for analyzing the evolutionary patterns of the neuraminidase gene of influenza A/H1N1 (2012)
  17. Cybis, G. B.; Lopes, Silvia R. C.; Pinheiro, H. P.: Power of the likelihood ratio test for models of DNA base substitution (2011)
  18. 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
  19. de Oliveira Martins, Leonardo; Kishino, Hirohisa: Distribution of distances between topologies and its effect on detection of phylogenetic recombination (2010)
  20. Durand, Pierre M.; Hazelhurst, Scott; Coetzer, Theresa L.: Evolutionary rates at codon sites May be used to align sequences and infer protein domain function (2010) ioport

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