[R-sig-phylo] Maximum-likelihood tree with continuous characters

Emmanuel Paradis Emmanuel.Paradis at mpl.ird.fr
Wed Aug 20 17:05:21 CEST 2008

Hi Mark,

Le 20.08.2008 13:02, Mark Ruddy a écrit :
> Dear all,
> is there a function/package available for maximum-likelihood tree  
> construction from continuous character data in R? I suspect there  
> isn't; mlphylo only accepts DNA models.

You're right on both points.

> Briefly, I have a large database of landmark data for geometric  
> morphometric analysis. I'm investigating relationships between  
> shapes. The only feasible approach to processing the data (bootstrap  
> from the original data>GM analysis>build a tree>repeat) is to script.  
> I have done this successfully in R with `nj' (neighbour-joining)  
> method but would like to try a maximum-likelihood method too.  
> Therefore, I suppose my fallback is to script R and PHYLIP's Contml  
> through the shell. Does anyone have any other suggestions?

You may script from R itself, writing your data matrix with 
write.table(), calling Contml with system(), and reading the tree back 
to R with read.tree().

Note that ape has ace() which can compute the likelihood of a single 
character but for a given tree only. You can imagine calling it 
repeatedly for each character and summing the log-likelihoods, but ape 
has no "tree traveller" at the moment (at least in R).



> Many thanks from a new R user,
> Mark Ruddy
> Ph.D. student
> Geography Department
> Royal Holloway
> University of London
> Egham
> Surrey
> TW20 0EX
> UK
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Emmanuel Paradis
IRD, Montpellier, France
   ph: +33 (0)4 67 16 64 47
  fax: +33 (0)4 67 16 64 40

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