Consensus tree of trees within 1% of best tree?

[Kelsey Pugh]

Hi there,

I'm trying to create a consensus tree from the top 1% of trees (ie. I only have one MPT, but would like to visualize all trees within a given number of steps of this MPT). This is fairly simple in PAUP, but I can't seem to figure it out in TNT. I've tried the BEST command, but so far all it's shown me is the one MPT.

Thanks in advance for any advice,
Kelsey

[Camilo Mattoni]

Hi Kelsey,
For to do that, first you must search for suboptimal trees.
Use the command 'SUBOPT N' (N is the number of extra steps for the suboptimal trees to keep), and search for suboptimal trees. After that, do a consensus.
Cheers,
Camilo

El 24/08/15 a las 16:22, Kelsey Pugh escribió:

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Camilo Mattoni
Laboratorio de Biología Reproductiva y Evolución
Instituto de Diversidad y Ecología Animal (IDEA, CONICET-UNC)
Facultad de Ciencias Exactas, Fisicas y Naturales
Universidad Nacional de Cordoba
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[Kelsey Pugh]

Hi Camilo,

Thanks very much for your response! When I tried SUBOPT, it gives this message: Suboptimal 4.000 x 0.000. Is it indicating that there are no trees within 4 steps of the shortest tree? Or am I just missing a step?

Thank you,

Kelsey

Kelsey Pugh
Ph.D Student
CUNY/ NYCEP
The Graduate Center, CUNY
365 Fifth Avenue
New York, NY 10016 USA

[Camilo Mattoni]

Hi Kelsey,
Subopt command only changes the settings of optimality.  You must search for trees.
E.g. Commands: subopt 4; bbreak;
will change the settings to keep trees 4 steps longer than the shortest, and will do a round of tbr branch swapping with the buffer trees. You can use mult por other search command here.
Cheers,
Camilo

[Kelsey Pugh]

Hi Camilo,

Thanks for your help. That worked perfectly.

Kelsey