re ci, ri, tree length

jonathan sheps gbga96 at udcf.gla.ac.uk
Mon May 15 10:55:00 EST 1995

In article <3p716i$4qk at mserv1.dl.ac.uk>, "Essop, FM, Dr"
<MFESSOP at chempath.uct.ac.za> wrote:

> I have noticed Mark Siddall's response to my "naive" questions 
> regarding ci's , ri's etc.   For his information, I have been doing 
> various analyses on my data set (with Hennig86) and found the results 
> confusing.  This confusion led to my questions regarding the EXACT 
> meaning of these indices.  When I performed such analyses at 
> different error values, Hennig86 produced different trees.  The 
> problem I've got is one of being totally objective in my analysis.   
> Which tree is the correct tree ?   I can actually select a tree to my 
> fancy - isn't this subjective ?   In the light of THESE observations, 
> I raised my questions as to what EXACTLY these values mean.  Where is 
> the cut-off value ?  How then should one "decide" what the best tree 
> is ?  These questions have unfortunately not been answered.  

I think Siddall gave you the exact meaning of these terms, but CI and RI
describe the homoplasy levels in the tree, they can't really be used to
compare trees generated from different data sets (though RI is closer to
being able to do this). For any given data set the shortest tree should
usually be the best one. How much longer than than the shortest you still
consider a 'reasonable" tree is up to you. I'm not sure what you mean by
"error values", but these must be altering your data set, and so giving
different trees. If so then you will have a family of shortest trees for
each error value, and how you choose the best error value I don't know.

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