[R-sig-phylo] GC content in light of nuclear polymorphisms

Good day all, I notice that the GC.content() function from the ape library discards both missing and 'unknown' sites from the calculation of percentage GC. I assume that 'unknown' sites refers to any base coded with the IUPAC codes (e.g. R,Y, W etc.). I have a nuclear dataset with 'known'

[R-sig-phylo] PICs in non-ultrametric trees

Dear all, I have a question on the use of scaling (standardizing contrasts). Liam remarked that in most cases you don't want unstandardized contrasts, but in which cases might I? I have a phylo-tree based on DNA barcode data, which means that the tree is not ultrametric (i.e. the tree does not

Re: [R-sig-phylo] PICs in non-ultrametric trees

Hi Peter, the non-standardized contrasts tells you how much sister lineages differ phenotypically (i.e., phenotype lineage A - phenotype lineage B) during the computation of contrasts (assumptions of brownian motion, etc). When you standardize them, you are dividing this difference by the

Re: [R-sig-phylo] GC content in light of nuclear polymorphisms

Hi Alastair, On 2/2/11, Alastair Potts pott...@gmail.com wrote: Good day all, I notice that the GC.content() function from the ape library discards both missing and 'unknown' sites from the calculation of percentage GC. I assume that 'unknown' sites refers to any base coded with the IUPAC