re ci, ri, tree length

Mark Siddall mes at zoo.toronto.edu
Tue May 16 23:56:54 EST 1995


In article <3p716i$4qk at mserv1.dl.ac.uk> "Essop, FM, Dr" <MFESSOP at chempath.uct.ac.za> writes:
>I have noticed Mark Siddall's response to my "naive" questions 
>regarding ci's , ri's etc.   For his information, I have been doing 

Hold on.  I never called them naive.  I was not denegrating.  I spent
a good deal of time trying to answer them.  I only suggested that the
nature of the query (being so basic) suggested a fundamental lack of
background.  Something that needed to be addressed beyond that of 
Usenet.  

>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 

You say "at different error values" but Hennig86 simply gives you the best 
(most parsimonious trees) for your data.  Period.  The only variation is in 
search algorithm.
With increasing probability of getting the most parsimonious trees:
h;
mh;
mh*;
mh;bb;
mh;bb*;
mh*;bb*;
ie-;
ie;
ie*;

Th only reaon for doing something less rigourous than something else above is 
time constraints.

Thus if you have done something more rigourous, then that is your best answer
and you can ignore the rest.

>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, 

You CANNOT select a tree to your fancy.  The more rigourous your use of Hennig86
the more likely to converge on a shorter tree or more trees of equal length.
This is spelled out in the Hennig86 manual.
The point is that given the same data, the shortest tree found is the best 
tree. Period.
The CI and RI ar e simply going to covary with that.
That is, a shorter tree for the same data will have a better CI and a
better RI than a longer tree for the same data. By definition.

>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.  

The best tree is the shortest tree you cn find.  If it does not take a week 
to run "ie;" then do it.  It will get you the shortest tree(s).

If there are multiple trees at the same length (by definition same CI and RI)
then they are all equally compelling.  You cannot and should not shoose.

Mark

>
>
>
>
>
>
>
>


-- 
Mark E. Siddall                "I don't mind a parasite...
mes at vims.edu                    I object to a cut-rate one" 
Virginia Inst. Marine Sci.                     - Rick
Gloucester Point, VA, 23062



More information about the Mol-evol mailing list