[R-sig-phylo] To plot a tree with mutation events on branches?

Sang Chul Choi Choi at Biology.Rutgers.Edu
Mon Apr 7 03:44:05 CEST 2008


I am wondering if I could draw a tree with mutation events on the  
branches of it. I saw many nice trees in Paradis APE R book (now I do  
not have access to that book any more unfortunately). This is a  
related question to that. I am also wondering if I could associate  
mutation events to a tree using phylo class.

What I want to do is to generate a coalescent tree using rcoal  
function and using branch length information with a scaled mutation  
rate parameter I want to randomly generate mutation events on the  
branches of the created genealogy. I was thinking that I could use  
phylo4 class of phylobase package. But, the document (http://ape.mpl.ird.fr/misc/FormatTreeR_4Dec2006.pdf 
) has a section: 4.4 Relating Nodes and Tips to Other Data. The  
section has a single sentence, and I cannot find further reading  
points. I guess that it may be possible to put mutation events on  
internal nodes somehow using ape package.

I will appreciate any input.

Thank you,

Sang Chul

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