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Embarrassingly basic question about cladistic analysis



Mike Taylor writes:
 > I'm sure plenty of people here can answer this ...
 > 
 > When a paper presents a cladistic analysis and says something like
 > "This analysis produced 72 equally most parsimonious trees (MPTs) with
 > length = 783, consistency index (CI) = 0.526 and retention index (RI)
 > = 0.687", where are the CI and RI values taken from?  Because as I
 > understand it, each of those 72 MPTs has its own CI and RI, correct?
 > Do people just pick one of the MPTs at random and report its
 > statistics?  Do they take the highest CI and the lowest RI that occur
 > in any of the MPTs?  Do they report the statistics of a consensus
 > tree?  Or what.

Oh dear.  Well, I did _say_ it was embarrassing.

I guess I must have been accidentally comparing CIs from consecutive
runs or something equally dumb.  I have now just checked the results
for 1000 of my MPTs, and they are all the same.  Also the RIs.  So
this whole issue is a non-issue.

Sorry to have wasted anyone's time.

 _/|_    ___________________________________________________________________
/o ) \/  Mike Taylor    <mike@indexdata.com>    http://www.miketaylor.org.uk
)_v__/\  "By filing this bug report you have challenged the honor of
         my family.  PREPARE TO DIE!" -- Klingon Programming Mantra