still confused about constraints

[Rutger Vos]

Dear all,

I am trying to run a tree search with a constraint tree based on the NCBI taxonomy (i.e. highly polytomous, with the idea being that the higher taxa are going to be monophyletic). The command reference on the wiki is ambiguous so I am unsure what to do:

force = (A (B C))

or:

force / (A (B C))

What is the difference? What is a "skeleton tree", which the wiki talks about: http://tnt.insectmuseum.org/index.php/Commands/force

I tried some searches with the '=' statement, but many genera are not recovered as monophyletic so this is not working as expected.

Thanks,

Rutger

[Martín Ramírez]

Hello Rutger, 

I think that force = (A (B C)) will force D outside, but force / (A (B C)) will allow D to be anywhere.

check if  "constrain = ; " is in effect when you do the search.

I hope it helps.

Martín

[Rutger Vos]

Hi Martin,

that makes sense, though the main problem I was actually having was that my parenthetical statements weren't quite right: nodes were being collapsed where they shouldn't be. Totally my own fault, TBH. Thanks!

Rutger

[pierre gousset]

Dear TNT users,

I am also trying to define constraints using the following type of code without success:

force / (A (B C))

As advised higher on this conversation, I checked for the activation of the constraints, and TNT returned me "constraints is ON", but after tree search, "constraints is OFF" was written just under (so before the command for the tree search itself in the text buffer). Additionally, the topology of the single most parsimonious tree I obtained does not satisfy my "force" command (in fact, adding that command to my .tnt file did not change anything to the tree I obtained). Does anyone know how to solve this?

Besides, the link (accessible here: https://web.archive.org/web/20140708070012/http://tnt.insectmuseum.org/index.php/Commands) explaining more about the "force" command seems to be dead. Does anyone know where / if I can get more information on that command?

Thank you in advance for your help.

Pierre Gousset

[Pablo Goloboff]

Dear Pierre, 

From what you say, it seems that you did not connect the constraints (constrain=; command), but you can also have screwed up in other ways (e.g. using "collapse auto" before searching, which is to say, "collapse trees after the search").

Please, send me the exact set of commands you used --otherwise, it's impossible for me to know if you have done anything wrong, or whether this is a bug.

Thanks, 

--Pablo 

[pierre gousset]

Dear Pablo,

Thank you for your answer. In fact, I found the solution to my issues, mainly thanks to a TNT tutorial written by Diego Pol and Hussam El Dine Zaher, whom I thank. I did not succeed to share the PDF file (is it possible to do it on this Google group?) so I just put at the end of this message the page that has helped me the most.

I also forgot to tick the "enforce constraints" box while doing the analysis.

Thanks,

Pierre