Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences.

By Beth Shapiro, Andrew Rambaut, Alexei J. Drummond. Molecular biology and evolution, 2006

761 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/2eb6b6f2bf07c4bd3e976b1c91b330e0b96c2eb1

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Citations in the corpus

PAML 4: phylogenetic analysis by maximum likelihood. (2007, methodology): “Application of such models in the ML method has been discussed by Yang (1996), Pupko et al. (2002), Shapiro, Rambaut, and Drummond (2006), and Bofkin and Goldman (2007).”
Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. (2012, background): “Choosing an appropriate partitioning scheme is a central problem for most phylogenetic analyses (Brandley et al. 2005; Shapiro et al. 2006; McGuire et al. 2007; Li et al. 2008; Blair and Murphy 2011).”
Major evolutionary transitions in ant agriculture (2008, methodology): “6 (70, 71) with the SRD06 two-partition codon-specific rates model of sequence evolution (72) and a Yule process for the tree prior.”
TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops (2008, methodology): “…2001) continues to gather pace with the development of faster and/or more sophisticated maximum likelihood (ML) and Bayesian inference methods, with recent software implementations including PhyML (Guindon and Gascuel, 2003), RAxML (Stamatakis, 2006) and MrBayes (Ronquist and Huelsenbeck, 2003).”
DEFINING THE MAJOR LINEAGES OF RED ALGAE (RHODOPHYTA) 1 (2006, background): “This approach appears to be superior to using a single set of rate parameters for protein-coding DNA sequences (Shapiro et al. 2005).”
Molecular phylogenetics: principles and practice (2012, methodology): “The rationale for data partitioning is to group genes or sites with similar evolutionary characteristics into the same partition so that all sites in the same partition are described using the same model, and different partitions use different models 89,90 .”
Selecting optimal partitioning schemes for phylogenomic datasets (2014, background): “Choosing an appropriate model of molecular evolution (model selection) is an important part of phylogenetics, and can affect the accuracy of phylogenetic trees, divergence dates, and model parameters [1-11].”
Integrating influenza antigenic dynamics with molecular evolution (2013, methodology): “Phylogenetic trees were estimated for A/H3N2, A/H1N1, B/Vic and B/Yam using BEAST [28] and incorporated the SRD06 nucleotide substitution model [83], a coalescent demographic model with constant effective population size and a strict molecular clock across branches.”
Global circulation patterns of seasonal influenza viruses vary with antigenic drift (2015, positive): “8.1 25 and incorporated the SRD06 nucleotide substitution model 26 , a coalescent demographic model with constant effective population size and a strict molecular clock across branches.”