Please HELP: How to run decay analyses

Knut Rognes (Knut Rognes) knutro at oslonett.no
Tue Jan 16 15:27:07 EST 1996


tosak at iastate.edu (Tosak Seelanan) wrote:

>I would appreciate any help in how to run decay analyses in PAUP
>(currently I have version 3.1.1) in case that the analyses have tree more
>than 32700 to save.  I do know that there is a way to get around with
>this situation by using constraint tree.  However, if any body can tell
>how exactly to do this, please e-mail me or post in this newsgroups.

I suggest that you
1. Create a treefile in the PAUP editor that contains the description of the trees
you want to use as constraints. The tree file can e.g. look like this:

#NEXUS
begin trees;
[filename: my.constraints
]
	translate
		1 taxon a,
		2 taxon b,
		3 taxon c,
		4 taxon d,
		5 taxon e,
		6 taxon f,
		;
tree first = ((1,2));
tree second = ((1,2,3));
tree third = ((1,2,3,4));
endblock;

2. Load this file (first item under the search menu) after you have executed the
data file. You can look at the constraint and check that it is the correct one by
selecting show constraints (also under the search menu).

3. Note that you do not have to list all taxa in the line describing a single
constraint tree, only the ones making up the group you are interested in.

4. Search; but be sure to check the optionenforce topological contstraints,
specify which constraint you want to use, e.g. tree second above and be sure to
check the button for keeping the shortest trees not satisfying the constraint i.e
not having the group (1 2 3). The length difference between the shortest tree and
the shortest not compatible with the constraint is the Bremer support (decay index
or whatever you want to call it).

Knut Rognes






More information about the Bio-soft mailing list