AVAILABLE: software for finding a particular tree among many

Mark Siddall mes at zoo.toronto.edu
Fri May 12 00:43:32 EST 1995

A while ago someone posted in this group a query about software 
that would find a particular tree among many trees.  
For those that are Hennig86 friendly, I have written such a program.
TRECMP.EXE will do a number of things.
1) find a defined tree among a suite (of any size) of any trees.
     - all that is needed for this is TRECMP.EXE and Hennig86
2) find the frequency of occurrence of a tree (in toto as opposed to
     clades of a tree) in bootstrap replicates.
     - for this you need to have created the replicates with my
       RandomCladistics program HEYJOE.EXE (which is freely
       available by anonymous ftp from zoo.toronto.edu as pub/random.exe)
3) it will also do automated Brooks Parsimony Analysis for biogeography
     and coevolutionary studies.

TRECMP.EXE is free to anyone who wants it.  For the time being email me and
   we'll arrange for a binary transfer or a diskette.  I will include 
   TRECMP.EXE in the next release of RandomCladistics (vers. 3) later
   in the summer.

1) portability - DOS only
2) reference tree - in parenthetical notation as for a Hennig86 treefile
      the file can be save from Hennig86 with tsave or created by
      the user.  e.g., 
                       tread (0(1(2(3 4))));
3) trees considered matching:
     i) any tree with the same topology irrespective of the order of
        taxa.  Thus both (0(1(2(3 4)))) and (0((3 4) 2) 1)) will
        match because they are same tree as will ((0 1)(2(3 4))) as it
        is the same tree just rooted differently.
     ii) in cases of unresolved nodes in the reference tree, any tree
        that represents any possible resolution of that polytomy [very
        interesting vis a vis bootstraps!].  Thus if the reference
        tree is (0(1(2 3 4))) this unresolved tree and any of 
        (0(1((2 3) 4))) (0(1(2 (3 4)))) or (0(1(3(2 4)))) will match.
        A fully resolved tree will only match itself.
        A fully unresolved tree will match everything.
4) suites of trees - as for (2) above.
5) occurrence in bootstrap replicates - replicates saved from HEYJOE.EXE 

Any takers?

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

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