tree length, ci, ri

Joe Felsenstein joe at evolution.genetics.washington.edu
Sat May 13 01:54:38 EST 1995

In article <3okk7g$ab7 at mserv1.dl.ac.uk>,
Essop, FM, Dr <MFESSOP at chempath.uct.ac.za> wrote:
>I have done some restriction mapping and constructed cladograms using 
>Hennig86.  I am not sure what the following values indicate: 
>i) consistency index - what for eg. does a ci value of 54 compared to 
>45 mean ?
>ii) retention index - same question as above
>iii) tree length - what for eg. does a tree length of 307 compared to 
>288 mean ?  How does one "decide" what the best tree is - based on 
>tree length ?

Mark Siddall characterized these as naive questions.  But I interpret them
as very substantive.  Sure a ci of 54 is better than 45, sure you can see
which value of a retention index is better than which, sure a shorter tree
is better than a long one.

But ... how much better?  Where is the cutoff?  If that is Essop's
questions then they are not naive at all, and I would like to know the

Joe Felsenstein         joe at genetics.washington.edu     (IP No.
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360

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