Fast likelihood calculations for comparative analyses

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mvmorph: an r package for fitting multivariate evolutionary models to morphometric data (2015, methodology): “Multivariate extensions of Pagel (1999) branch-length transformations are proposed in MOTMOT (Thomas & Freckleton 2012; no more on the CRAN repository but accessible from the archive); BM with multiple evolutionary rate matrices can be ﬁtted with evol.vcv as well as a phylogenetic canonical…”
A linear-time algorithm for Gaussian and non-Gaussian trait evolution models. (2014, methodology): “We focus here on the model proposed by Freckleton (2012), where each trait is assumed to follow Pagel’s model with phylogenetic signal k for trait k, using cov(Yi,k,Yj, )=Ck Vij( √ k ) for traits k, and taxa i,j (Freckleton 2012, Supporting Information).”
Geiger V2.0: an Expanded Suite of Methods for Fitting Macroevolutionary Models to Phylogenetic Trees (2014, methodology): “…3 in Supplementary Material for details) to correct for multiple comparisons—the larger the phylogeny, the greater the threshold for accepting a new partition to the model [a similar approach was developed by Thomas and Freckleton (2012) for studying variation in rates of phenotypic evolution].”