newick trees with polytomies as input

[kmeusemann]

Dear all, just a quick question: can ASTRAL handle also trees (newick) with polytomies while other branching pattterns are present (with supoort values)? If so, does within Astral estimation of the species tree also the branch length does play a role or not? (asking because when I'd use as input a tree where I have previously contracted/collapsed clades due to a low support value , its actually a bit artificial isn't it?

• Would you recommend it or rather not?

[smirarab]

On Wed, Jan 15, 2020 at 3:11 AM kmeusemann notifications@github.com wrote:

Dear all, just a quick question: can ASTRAL handle also trees (newick) with polytomies

Yes.

while other branching pattterns are present (with supoort values)?

Not sure what you mean.

If so, does within Astral estimation of the species tree also the branch length does play a role or not?

Again, not fully sure what you are asking. But ASTRAL does not use branch length in the input trees.

(asking because when I'd use as input a tree where I have previously contracted/collapsed clades due to a low support value , its actually a bit artificial isn't it?

Not sure what you mean. Please see the paper below.

Zhang, Chao, Maryam Rabiee, Erfan Sayyari, and Siavash Mirarab. 2018. “ASTRAL-III: Polynomial Time Species Tree Reconstruction from Partially Resolved Gene Trees.” BMC Bioinformatics 19 (S6): 153. https://doi.org/10.1186/s12859-018-2129-y.

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-- Siavash Mirarab

[kmeusemann]

Dear Siavash, thanks for your reply, y you solved my questions with your answers.

Any recommandations for a tool/software where I can easily collapse low supported clades to polytomies? (automaticaly for a bunch of gene trees - ewick format and unrooted for example on command line?

[smirarab]

I like to use newick utilities: http://cegg.unige.ch/newick_utils

nw_ed inputgenetrees.tre 'i & b <= 0.10' o > contracted-10-genetrees.tre

On Thu, Jan 16, 2020 at 2:36 AM kmeusemann notifications@github.com wrote:

Dear Siavash, thanks for your reply, y you solved my questions with your answers.

Any recommandations for a tool/software where I can easily collapse low supported clades to polytomies? (automaticaly for a bunch of gene trees - ewick format and unrooted for example on command line?

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-- Siavash Mirarab

[kmeusemann]

Many thanks!! Best, Karen