constrained tree search approach

[Jacopo Martelossi]

Hi all,

i would like to carry out a constrained tree search to abtain a tree with specific relationship  between clades, but without being interested in internal relations and then perform a topological test between the result obtained and another tree. Is the approach to write a newick file with politomies fo each clade correct?

Thank you in advance for the help.

Best 

Jacopo

[Minh Bui]

Hi Jacopo,

It’s not clear to me, which trees are you comparing. 

But are you comparing a fully bifurcating tree with a polytomy (multifurcating) tree?

If yes, I think this is unfair for the polytomy tree. 

A fully bifucating tree has 2n-3 branch lengths (n=#taxa). Whereas a multifurcating tree has fewer branch lengths, thus will tend to have lower log-likelihood and be likely rejected.

Therefore, I would fully resolve the multifurcating tree by e.g. a constrained tree search. And then compare the resolved tree with the other bifurcating tree.

Does that answer your question?

Minh

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[Jacopo Martelossi]

Hi,

thank's for the explanation,yes my idea was to use a multifurcating tree as constrains just because i'm not interested in the internal relathionship of the clades, making them resolved with the constrain tree search and then compare the result with others bifurcating trees. I've tried a search with an input constrain tree like ((((A,B,C,D),(F,G,H,I)),((L,M,N,O),(P,Q,R,S))),(U,V,Z)); but i get the error message "constrain tree must be unrooted", how can i solve it?

 Thank you for your patience and helpfulness.

Jacopo.

Il giorno venerdì 7 giugno 2019 02:34:12 UTC+2, Minh Bui ha scritto:

Hi Jacopo,

It’s not clear to me, which trees are you comparing. 

But are you comparing a fully bifurcating tree with a polytomy (multifurcating) tree?

If yes, I think this is unfair for the polytomy tree. 

A fully bifucating tree has 2n-3 branch lengths (n=#taxa). Whereas a multifurcating tree has fewer branch lengths, thus will tend to have lower log-likelihood and be likely rejected.

Therefore, I would fully resolve the multifurcating tree by e.g. a constrained tree search. And then compare the resolved tree with the other bifurcating tree.

Does that answer your question?

Minh

On 6 Jun 2019, at 6:57 pm, Jacopo Martelossi <jacopo.m...@gmail.com> wrote:

Hi all,

i would like to carry out a constrained tree search to abtain a tree with specific relationship  between clades, but without being interested in internal relations and then perform a topological test between the result obtained and another tree. Is the approach to write a newick file with politomies fo each clade correct?

Thank you in advance for the help.

Best 

Jacopo

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[Minh Bui]

Hi Jacopo,

Which version are you using? Can you please try the latest version?

This restriction has been lifted, I think.

Minh

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[Minh Bui]

Hi Jacopo,

This problem was discussed and answered here: https://groups.google.com/forum/#!topic/iqtree/o-Fmnfo1WBI

And sorry, I thought this was changed, but only in the beta version 1.7.

Minh

On 12 Jun 2019, at 10:54 pm, Jacopo Martelossi <jacopo.m...@gmail.com> wrote:

i've download the last version 1.6.11, but i've recived the same error message.