Problems applying hard constraint tree to a fossil maximum likelihood tree

[Harriet Nuttall]

Hello,

I'm hoping someone might be able to help me with an issue I'm encountering using constraints. In summary, the constraint tree which is appended to the .tnt file applies, but does not apply strongly enough, such that the resulting output tree has polytomies where it ought to have resolution. 

I've been fiddling with the command code today, changing the collapse command to different options, but with no effect. TNT confirms each time that it has registered the collapse command change, but the tree result is the same. The code I have ended up with is below. Does anybody have any ideas? Thank you!

taxname =;
mxram 1023;

log supertree_log.txt
proc mrp_matrix_full.tnt;
force/&0;
constrain=;
outgroup allzero;
hold 50000;
xmult=level10;
bbreak=fillonly;

nelsen*;
collapse -;
export=trees.tre;

[Martín Ramírez]

Hello Harriett, 

If the constraint tree is resolved but the resulting tree is not, perhaps what is missing is synapomorphies for the unresolved clades. Then TNT will collapse zero-length branches. Perhaps a way of testing this is inserting a line "collapse 0;"  after the mxram line. 

Good luck!

Martin

[Harriet Nuttall]

Thank you so much Martin, that worked very well :) I hadn't realised that I needed to specify the collapse rule at both ends of the analysis!

[Buz Wilson]

Hello TNT group
It seems that UBUNTU 24.04 doesn't have pvm in the repositories, and I
can't get the binaries provided with the TNT installation to run. What
24.04 does have is now KVM but I suspect TNT doesn't know how to work
with that. I'll be looking at getting MPI running.
Any other suggestions?
Buz
(now running TNT in one core on a 32 thread machine).

--
George D.F. (Buz) Wilson, Ph.D.
Saugatuck Natural History Laboratory, LLC
publications: www.researchgate.net/profile/George-Wilson-12
email: gdfw@SNHLab com

[nycac...@gmail.com]

If I remember Dan Janies’ work, you van sneaker parallel.
Just spin up 100 randomized searches, then that their tree files, swap and fuse


Thumbtyped or badly dictated by
Mark Siddall,


> On Sep 5, 2025, at 11:09 AM, Buz Wilson <buzw...@gmail.com> wrote:
>
> Hello TNT group

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[Martín Morales]

Hi.

Apparently you have a problem with the TNT installer. I suggest manual installation. There is a document to perform it. Check the downloaded package.

Best regards,

Martín