I just discovered that the phytools article has been officially published in Methods in Ecology & Evolution. The article, like all program notes published in MEE, is available "open access" (link to article here). Check it out.
The article is already "out of date," in the sense that its list of phytools functionality leaves out many new features in the package, nonetheless some users might find the worked examples (which includes vignette style code from an interactive R session) helpful in guiding their use of some of phytools' functions.
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