IQTree2 bootstrap and polytomies

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Bálint Márk Vásárhelyi

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Aug 3, 2020, 1:03:38 AM8/3/20
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I used iqtree2 -s masked_alignment.fasta -m GTR -T 30 -fast -redo -czb -b 100 to construct a tree with bootstrap values.
It is strange that the consensus tree has both bootstrap values and polytomies. Is it possible to show only the bootstrap values and resolve all polytomies?



Bálint Márk Vásárhelyi

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Aug 3, 2020, 1:09:20 AM8/3/20
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I also tried the command without '-czb', and there are still polytomies.

Minh Bui

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Aug 5, 2020, 7:09:16 PM8/5/20
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Hi there,

The consensus tree might indeed have polytomy. So that’s not unexpected.

If you want strictly bifurcating tree, then look at the ML tree. 

Cheers
Minh


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