[BiO BB] getting a phylogenetic tree w/distances

James Cotton j.a.cotton at qmul.ac.uk
Tue Aug 21 11:36:10 EDT 2007

Depends on what you mean by distances, really: distances on molecular  
phylogenies are usually estimates of sequence divergence, and so  
depend on what gene is used to build the phylogeny. That might not be  
ideal for what you want: is the software sensitive to the absolute  
scale of the branch lengths, or just their relative sizes?

If the latter, you could use the estimated divergence ages of the  
different taxa to put branch-lengths on your tree - i.e. have branch  
lengths in terms of millions of years since the divergence of the  
groups. you can find some estimates of those numbers in e.g. this  
paper: http://www.ncbi.nlm.nih.gov/sites/entrez? 
cmd=Retrieve&db=PubMed&list_uids=9582070, Though these estimates  
might be a bit out-of-date now.

If the software is sensitive to the absolute scale of the branch  
lengths, I guess you need some kind of "mean sequence divergence"  
between the taxa, which is probably around in the literature  
somewhere, but I don't know where.. There are some estimates in  
textbooks e.g. Li's Molecular Evolution book, but I'm not sure you'll  
find all the numbers, and even then, they might not fit on a tree -  
perhaps someone else knows a tree with these figures already attached?

Hope this helps,

On 21 Aug 2007, at 04:44, Ilya Shlyakhter wrote:

> Where can I get a phylogenetic tree, with distances for all branches,
> for the organisms { mouse, rat, dog, cow, human }?  I can get the
> structure of the tree from ToLWeb.org, but not the distances; and
> TreeBASE.org doesn't have a tree for this specific set.  I need the
> tree for use with a phylogeny-aware Gibbs motif finder.
> Thanks for help,
> Ilya
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James Cotton
School of Biological and Chemical Sciences
Queen Mary, University of London
+44 (0)207 882 8287
j.a.cotton at qmul.ac.uk

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