More classical site-homogeneous models are also implemented, such as JTT (Jones et al., 1992), WAG (Whelan and Goldman, 2001) or LG matrices (Le and Gascuel, 2008), for proteins, and the general time-reversible (GTR) model for protein and nucleic acid data. Gathering several recent developments about the use of mixtures in statistical phylogenetics, PhyloBayes 3 proposes a wide range of models accounting for site-specific variations of several features such as: Overall, PhyloBayes 3 makes it possible to use a large spectrum of substitution models for both phylogenetic reconstruction and molecular dating analyses. As its two main distinguishing features, this program gathers a large class of recently published models accounting for variations of the substitution patterns along the sequences, and rate variations along lineages (relaxed clocks). In this direction, we propose a Bayesian phylogenetic reconstruction program, PhyloBayes 3. Yet, current molecular dating software packages do not implement such sophisticated substitution models. In particular, mixture models of amino acid replacement have resulted in important advances in model fit and phylogenetic reconstruction (Lartillot et al., 2007 Le et al., 2008b Wang et al., 2008), suggesting that their use in molecular dating analyses may also result in fundamental improvements. ![]() However, many of these developments are often available through distinct implementations, sometimes under different statistical paradigms (maximum likelihood versus Bayesian), making comparative evaluations more difficult, and preventing potentially powerful model combinations to be applied to empirical data. Many new models have been proposed, such as mixture models, accounting for site-specific effects (Huelsenbeck and Suchard, 2007 Lartillot and Philippe, 2004 Le et al., 2008a, b Pagel and Meade, 2004 Wang et al., 2008), or flexible molecular clocks (Drummond et al., 2006 Lepage et al., 2007 Thorne et al., 1998). The field of phylogenetics has been particularly prolific over the recent years.
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