Re: [R-sig-phylo] AGY coding

Hi Karla. Not sure how you have your sequences stored, but if as a string you can do it yourself: str <- gsub("C|T", "Y", str); As for RY vs. AGY, this paper is very nice. Basically, if you are using them for

Re: [R-sig-phylo] Aligning tree tip labels together in ape

Hi Nick. The following is a 'solution' that works with phytools; however, you should keep in mind that you will not generally be able to use a constant offset value if your tip labels vary in length. In that case, you would either have to use a variable offset or figure out the minimum

Re: [R-sig-phylo] Aligning tree tip labels together in ape

Hi Nick, There is a fantastic package for visualizing trees, the "ggtree" package: https://github.com/GuangchuangYu/ggtree Here is a vignette with several examples on how to display trees, including your circular phylogram visualization:

[R-sig-phylo] AGY coding

Dear all, Does anyone have a function for AGY coding of nucleotides? By the way, any thoughts on using RY- vs AGY-coding? Thanks! Karla [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org