phylogenetic reconstruction using infinite mixtures

PhyloBayes (Lartillot et al, 2009) is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction. Compared to other phylogenetic MCMC samplers, the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT (Lartillot and Philippe, 2004). CAT is an infinite mixture model accounting for site-specific amino-acid or nucleotide preferences. It is well suited to phylogenomic studies using large multigene alignments.

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correlated evolution of substitution rates and quantitative traits

Coevol (Lartillot and Poujol, 2011) is a Bayesian MCMC program for doing comparative analyses combining molecular data and quantitative traits. The program takes as an input a multiple sequence alignment, a matrix of quantitative traits (e.g. ecological variables or life-history traits), a phylogenetic tree, and fossil calibrations. It then simultaneously reconstructs the phylogenetic history of the quantitative traits, and of certain key parameters of the substitution process (e.g. the rate of substitution, the dN/dS ratio, or the equilibrium GC content); estimates the correlations between the quantitative traits and the substitution parameters (corrected for phylogenetic inertia); and reconstructs divergence times.

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Using coevol for reconstructing the phylogenetic history of Ne

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