Phylogenetic Analysis by Maximum Likelihood (PAML)

By Ziheng Yang. 2002

379 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/ebee9548aee4567cc3cbbde131d54d3bc5a0fca9

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Citations in the corpus

An index of substitution saturation and its application. (2003, methodology): “We use the program EVOLVER in the PAML package (Yang, 2000) for the evolutionary simulation.”
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. (2003, background): “Anisimova, M., J. P. Bielawski and Z. Yang, 2002 Accuracy and Polley, S. D., and D. J. Conway, 2001 Strong diversifying selection power of Bayes prediction of amino acid sites under positive on domains of the Plasmodium falciparum apical membrane antiselection.”
Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes (2004, methodology): “After removing gaps and N-containing codons, the level of synonymous substitution was estimated using the maximum likelihood method implemented in codeml (Yang, 1999) under the F3x4 model (Goldman and Yang, 1994).”
Molecular taxonomy, origins and evolution of freshwater ascomycetes (2006, methodology): “In brief, the dataset was subject to maximum likelihood analyses using the modules BASEML in the PAML 3.12 program package (Yang, 1997), using the tree shown in Fig.”
Detecting putative orthologs (2003, methodology): “Then, using Clustalw (Thompson et al., 2000), each protein sequence in H is aligned separately with the original query sequence i. If the alignable region of the two sequences exceeds a threshold fraction of the alignment’s total length (0.8 is our working cutoff), the program PAML ( Yang, 2000 ) is”