PAML4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591.Yang Z. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24:1586-91.Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24: 1586-1591....
PAML (Phylogenetic Analysis by Maximum Likelihood)This article has no abstract.doi:10.1002/0471650129.dob0515Michael P. CummingsJohn Wiley & Sons, Inc.
PAML 4: Phylogenetic Analysis by Maximum Likelihood PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs m... Z Yang - 《Molecular Biology & Evolution》 被引量: 1.2万发表: 2007年 PAML 4:...
PAML 4: a program package for phylogenetic analysis by maximum likelihood.Yang, Z
This paper describes a parallel application for phylogenetic analysis of DNA sequences. The program extends the phylogenetics program Trexml to increase the speed of this rather exhaustive tree searching program. The program uses the Advanced Stepwise Addition Algorithm (ASA) and provides two main adva...
(2016) Mutation rate analysis via parent-progeny sequencing of the perennial peach. I. A low rate in woody perennials and a higher mutagenicity in hybrids. Proc Biol Sci 283:1841 Google Scholar Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591...
The codeml program of the PAML (Phylogenetic Analysis by Maximum Likelihood; [37];) 3.15 software package was applied to test for positive selection. PAML uses a maximum likelihood algorithm to assign likelihood scores to different models for selection. If a model incorporating positive selection gav...
Yang Z: PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007, 24: 1586-1591. 10.1093/molbev/msm088. PubMed CAS Google Scholar Yang Z, Nielsen R: Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol. 2000, 17: 32-...
(Bayesian Information Criterion) to the model selection in maximum-likelihood phylogenetic analyses. Reliability of maximum-likelihood trees was examined by bootstrap analysis based on 1000 replicates. Polychotomies were generated by collapsing the nodes with a bootstrap value lower than 50. We mainly...
phangorn is a package for phylogenetic reconstruction and analysis in the R language. phangorn offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation. Extending the general ML framework, this package...