[R-sig-phylo] Rooting on a node with resolve.root = TRUE

Carvalho PhD student, Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, Ash 2, office 123 University of Edinburgh, United Kingdom. http://br.linkedin.com/pub/luiz-max-carvalho/49/687/283 [[alternative HTML version deleted

[R-sig-phylo] Count the number of character/state changes in a tree

? Thanks in advance, Luiz -- Luiz Max Fagundes de Carvalho PhD student, Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, Ash 2, office 123 University of Edinburgh, United Kingdom. http://br.linkedin.com/pub/luiz-max-carvalho/49/687/283

[R-sig-phylo] Potential glitch in phymltest

this minor issue. Cheers, Luiz -- Luiz Max Fagundes de Carvalho PhD student, Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, Ash 2, office 123 University of Edinburgh, United Kingdom. http://br.linkedin.com/pub/luiz-max-carvalho/49/687/283

Re: [R-sig-phylo] Sampling bias in discrete trait estimation

interesting follow-ups one could do here. cheers, matt On Mon, Nov 11, 2013 at 9:52 AM, Luiz Max Carvalho luizepidemiolo...@gmail.com wrote: Dear all, Suppose you have observed K discrete traits for a phylogeny with N tips. For some reason, you think your trait sampling is not random, i.e

[R-sig-phylo] Does anyone know about a function to remove redundancy from a database?

I've been looking for a function that could scan a DNAbin object and return just the unique sequences. Does anyone know about a function for that? Thanks in advance, -- Luiz Max Fagundes de Carvalho, IC, Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Rio de Janeiro, Brasil.

Re: [R-sig-phylo] Does anyone know about a function to remove redundancy from a database?

Great! Thank you! 2013/2/19 Klaus Schliep klaus.schl...@gmail.com Hi Luiz, phangorn has a generic unique function for phyDat objects. There may be more elegant ways, but this code should work: library(phangorn) y = as.DNAbin(unique(as.phyDat(x))) Cheers, Klaus On 2/19/13, Luiz Max