why topological constraint tree file (-g) doesn't work ?

[George Nancy]

Hi Minh.

These days, I want to constraint the tree's topology. So I use this command : -g , but the result seems like it didn't use this input file.

Environment: macOS iqtree2.1.3

command: bin/iqtree2 -s 106_3_yeast.phy -m 12.12 -g 106_3_yeast.phy.treefile -pre 106_new

input files:

-g 106_3_yeast.phy.treefile:  (Scas,(Sklu,Calb));

output  treefile: ((Scas:0.1974400426,Sklu:0.1995698673):0.2168951579,Calb:0.1594746925):0.0000000000;

 

when i didn't use the command -g with the input treefile, the result is the same as before.

So, Minh, I use the wrong command or other reasons?

Thank you!

Best wishes!

Nancy

[Minh Bui]

Hi Nancy,

Because the constraint tree will be UNROOTED.

In your case, (Scas,(Sklu,Calb)); is the same as ((Scas,Sklu),Calb);. After unrooting, both trees become (Scas,Sklu,Calb);.

Which means, with just 3 taxa, there is actually no constraint. You need at least 4 taxa for constraint to be effective.

However, in your case you have just 3 taxa in the alignment, so you don’t really need the constraint, just use it as input tree and compute the likelihood: simply change -g to -te:

bin/iqtree2 -s 106_3_yeast.phy -m 12.12 -te 106_3_yeast.phy.treefile -pre 106_new

Contraint tree is only useful either when there are fewer taxa in the constraint than total taxa or there are multifurcation in the constraint tree or both.

Moreover, I can see the merit here: you have a non-reversible model (12.12) and want to test the root position, right?

In that case, there is already an option for you, see: http://www.iqtree.org/doc/Rootstrap

Minh

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