TNT Character setting

[Plateau olivia]

Dear all,

On TNT I saw that it was possible to say that our characters are "order" or "unorder" but not "reversible" or "irreversible".

Or  I need to add the condition "irreversible" for some characters to say that, for example, only the changes from 0 to 1 and 1 to 2 are possible and not 2 to 1.

It's also possible to impose this condition in Mesquite. But, when the file is read in TNT its not take into account.

Do you know if there is a way in TNT to do this? 

Thanks a lot !

Olivia

[Nick Matzke]

I forget how cost matrices work in TNT, but if you set some large cost for the "irreversible" step, this is effectively the same as making the transition irreversible.

E.g. maybe the cost is 1 step for losing flight, but 100 steps for regaining flight.

Cheers,

Nick

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[Camilo Mattoni]

Hi Olivia,

You can implement a Sankoff step-matrix in TNT with the Data/Character settings menu, or using the command 'smatrix', and with 'ccode' and the option ( for to indicate which character will use the Sankoff matrix. See below how this can be applied in the matrix file, for the character 3, with 1 step for state 0 to 1 and 100 steps for 1 to 0:

Ccode 
   (  3

COMMAND: SMATRIX
smatrix =0 (StepMatrix0)
      0>1  1     1>0  100 
     ;

Cheers,

Camilo

El 28/1/19 a las 17:50, Nick Matzke escribió:

-- 
__________________________________________________
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
Av. Velez Sarsfield 299
5000 Cordoba
ARGENTINA
camilo...@unc.edu.ar
camilo...@gmail.com
Phone: (54) 351 3571921
http://www.labre.com.ar
__________________________________________________

[Plateau olivia]

Thanks a lot, I will try in any cases!

Best regards,

Olivia

Le lundi 28 janvier 2019 22:36:05 UTC+1, Nick Matzke a écrit :

I forget how cost matrices work in TNT, but if you set some large cost for the "irreversible" step, this is effectively the same as making the transition irreversible.

E.g. maybe the cost is 1 step for losing flight, but 100 steps for regaining flight.

Cheers,

Nick

On Tue, Jan 29, 2019 at 6:26 AM Plateau olivia <olivia....@gmail.com> wrote:

Dear all,

On TNT I saw that it was possible to say that our characters are "order" or "unorder" but not "reversible" or "irreversible".

Or  I need to add the condition "irreversible" for some characters to say that, for example, only the changes from 0 to 1 and 1 to 2 are possible and not 2 to 1.

It's also possible to impose this condition in Mesquite. But, when the file is read in TNT its not take into account.

Do you know if there is a way in TNT to do this? 

Thanks a lot !

Olivia

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Para cancelar la suscripción a este grupo y dejar de recibir sus mensajes, envía un correo electrónico a tnt-tree-analysis-using-new-technology+unsubscribe@googlegroups.com.
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