Program for tree comparison

Joe Felsenstein joe at evolution.genetics.washington.edu
Thu Apr 20 00:56:01 EST 1995

In article <3n2k2k$rmp at sunserver.lrz-muenchen.de>,
Korbinian Strimmer  <strimmer at zi.biologie.uni-muenchen.de> wrote:
>I am happy
>read that John Huelsenbeck has a functioning C routine designed precisely
>for the purpose of tree comparison. The obstacle that "..the program is
>very user friendly (I am currently the only user).." should be easily
>removable.  I haven't seen the code yet but if it is not too complicated
>I would volunteer to add a menu from the sort of the PHYLIP menus to his
>program to overcome this, so that everybody can do tree comparisons
>with ease.

This discussion has also moved me towards some generalization of CONSENSE
in the 4.0 release of PHYLIP (not due soon, alas).  But what puzzles me is
what features people need.  I guess we need to be able to read in a file
of trees and make a variety of kinds of consensus trees among them.
But as for tree distances, how would users want the input trees to be fed
in?  In pairs in the same file?  In two files, whose corresponding members
get compared?  In two files, one with one tree and another with many,
each of which is to be compared to the one tree?

I guess the answer is "all of the above, as options".  If anyone has
a feeling as to which is the "natural" method input of trees to such a
consensus-and-tree-distance tool, do let us know.

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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