Computational Molecular Evolution

By Ziheng Yang. 2006

483 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/fd0d5a31105fe09db112ba7db0b4793bc150064f

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In Genetics

Citations in the corpus

Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution (2008, unknown): “rates and transition/transversion rate ratios were computed by maximum likelihood with PAML (Yang, 2006; Yang, 1997) using a physical-sites definition (Bierne and Eyre-Walker, 2003) operating on codons (codeml program) with the F3×4 codon frequency model, one dN/dS ratio per branch (model 0), and an”
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis (2018, methodology): “Other substitution and site models added are the polymorphism-aware model (PoMo) [11, 22] (which can account for within-species variation and GC-biased gene conversion), pseudo Dollo [51], codon models [17, 52], standard named nucleotide models (SSM package), standard empirical amino acid models (OB”
Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees (2014, methodology): “ve that changes the position of a transition is equal to min(1, L). 13 To update any of the zero-bounded rate parameters in the model (Λ, λ i, µ i), I used a proportional shrinking-expanding proposal [42], such that 260 r'=reη(U−0.5) (8) where r is the current value of the rate parameter, U is ”
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences (2021, methodology): “Taking the HKY model [30] as an example, therefore, Kn can be deduced from the observed transitional and transversional substitutions ( S and V , respectively) as well as four nucleotide frequencies ( p A , p T , p G , and p C ) , according to Equation (1) (see Equations 1.27 and 1.28 in [31]).”
Phylogenetic Methods in Biogeography (2011, methodology): “Model parameters are estimated using an appropriate data set and either ML or Bayesian inference (BI) principles (Felsenstein 2003, Holder & Lewis 2003, Ronquist & Deans 2010, Yang 2006); only a brief summary of these approaches is given here.”
An improved general amino acid replacement matrix. (2008, methodology): “More details and explanations can be found in textbooks (e.g., Felsenstein 2003; Bryant et al. 2005; Yang 2006).”