bootstrap value missing

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Alex Cussigh

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Aug 18, 2020, 8:19:46 AM8/18/20
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Hello everyone,
I think I have a problem with bootstrap values in some trees made using fish nsbi sequences.
In all my trees, after I rooted using the outgroup, the first node after the root (which is normal that it has not the bs value) always misses its bootstrap value.
Is it an issue or is it normal?
I've attached the iqtree file of the simplest tree and also the tree visualized using FigTree (the outgroup is HM392103.1).
I hope I made myself clear, sorry if this question seems dumb to you all.
Alex

seq_SL_coi_23_05_20_aligned.fasta.iqtree
Schermata 2020-08-18 alle 14.12.31.png

Olga Chernomor

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Aug 18, 2020, 8:36:27 AM8/18/20
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Dear Alex,

the reason is that the mentioned bootstrap value is 100 by default, because it separates only one species from the rest and is present in all trees. If you root the tree with an outgroup containing more than one species, the bootstrap value will be present.

Best wishes,
Olga

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<seq_SL_coi_23_05_20_aligned.fasta.iqtree><Schermata 2020-08-18 alle 14.12.31.png>

Alex Cussigh

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Aug 19, 2020, 12:51:06 PM8/19/20
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Thank you Olga for the reply.
But maybe I did not make myself clear. My issue does not regard the branch which leads to Rutilus rutilus since it is the point in which I rooted the tree, but the node which leads to KJ552335 which is the most basal group and it does not have any bootstrap value

Olga Chernomor

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Aug 20, 2020, 6:53:55 AM8/20/20
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Hi Alex,

sorry, I misread the original message. Then this is an issue of visualisation actually. Just try rooting with other species to see the support for two taxa (KJ552335, HM392103), or you can also look it up in the file itself. Here is a different rooting of your tree, you can see that the bootstrap for (KJ552335, HM392103) is 92.

sFtov-Sa4EqVphvN-tX0Tw.pdf

Olga Chernomor

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Aug 20, 2020, 7:01:16 AM8/20/20
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Hey again:)

even more simple, the bootstrap I mentioned (support of clustering KJ552335 with HM392103) is actually the one stated for the next clade. So it is the visualisation, that tricks the mind:) To reply your original message, it is normal that you do not observe the value right after the root. Sorry for the messy replies.

Cheers,
Olga



On 20.08.2020, at 12:53, Olga Chernomor <o.che...@gmail.com> wrote:

Hi Alex,

sorry, I misread the original message. Then this is an issue of visualisation actually. Just try rooting with other species to see the support for two taxa (KJ552335, HM392103), or you can also look it up in the file itself. Here is a different rooting of your tree, you can see that the bootstrap for (KJ552335, HM392103) is 92.

<sFtov-Sa4EqVphvN-tX0Tw.pdf>

Cheers,
Olga



On 19.08.2020, at 18:51, Alex Cussigh <dottor...@gmail.com> wrote:

Thank you Olga for the reply.
But maybe I did not make myself clear. My issue does not regard the branch which leads to Rutilus rutilus since it is the point in which I rooted the tree, but the node which leads to KJ552335 which is the most basal group and it does not have any bootstrap value

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