Re: [raxml] boot strap
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Alexandros Stamatakis
Sep 29, 2022, 4:47:04 AM9/29/22
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Dear Florinda,
It would be interesting to know the difficulty score of your dataset,
please see here for a paper describing the tool and method:
https://www.biorxiv.org/content/10.1101/2022.06.20.496790v1
Also your BI tree seems to have many multifurcations, could it be that
you have very small branch lengths in your tree?
Alexis
On 29.09.22 10:24, Florinda D'Archivio wrote:
> I am doing a phylogenetic analysis with a partitioned dataset, with 20
> taxa and 1300 characters. With the ML analysis done with raxml I obtain
> bootstrap values which are very low (tree on the right), while with BI
> performed in MrBayes most of the PP are acceptable (tree on the left).
> Could increasing the number of taxa help in this?
> Sorry for asking this, I am a begginer in phylogenetics.
>
> Thank you
>
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--
Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP) lab,
Institute of Molecular Biology and Biotechnology, Foundation for
Research and Technology Hellas
www.exelixis-lab.org
It would be interesting to know the difficulty score of your dataset,
please see here for a paper describing the tool and method:
https://www.biorxiv.org/content/10.1101/2022.06.20.496790v1
Also your BI tree seems to have many multifurcations, could it be that
you have very small branch lengths in your tree?
Alexis
On 29.09.22 10:24, Florinda D'Archivio wrote:
> I am doing a phylogenetic analysis with a partitioned dataset, with 20
> taxa and 1300 characters. With the ML analysis done with raxml I obtain
> bootstrap values which are very low (tree on the right), while with BI
> performed in MrBayes most of the PP are acceptable (tree on the left).
> Could increasing the number of taxa help in this?
> Sorry for asking this, I am a begginer in phylogenetics.
>
> Thank you
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
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> <mailto:raxml+un...@googlegroups.com>.
> To view this discussion on the web visit
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> <https://groups.google.com/d/msgid/raxml/eb53cbc6-11da-43c2-b9ef-adc78b0925b0n%40googlegroups.com?utm_medium=email&utm_source=footer>.
--
Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP) lab,
Institute of Molecular Biology and Biotechnology, Foundation for
Research and Technology Hellas
www.exelixis-lab.org
Florinda D'Archivio
Sep 29, 2022, 5:10:32 AM9/29/22
to raxml
Thank you for reply!
I will check the article, thanks!
Yes the branch lengths are actually very small...
Alexandros Stamatakis
Sep 29, 2022, 6:50:43 AM9/29/22
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The small branch lengths could be part of what you are observing for
sure. Are those very closely related sequences? Did RAxML potentially
report even exactly identical sequences?
Alexis
> <https://groups.google.com/d/msgid/raxml/eb53cbc6-11da-43c2-b9ef-adc78b0925b0n%40googlegroups.com?utm_medium=email&utm_source=footer
> <https://groups.google.com/d/msgid/raxml/e5480a72-7f86-4354-ba92-1d122368e549n%40googlegroups.com?utm_medium=email&utm_source=footer>.
sure. Are those very closely related sequences? Did RAxML potentially
report even exactly identical sequences?
Alexis
> <https://groups.google.com/d/msgid/raxml/eb53cbc6-11da-43c2-b9ef-adc78b0925b0n%40googlegroups.com?utm_medium=email&utm_source=footer>>.
>
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP)
> lab,
> Institute of Molecular Biology and Biotechnology, Foundation for
> Research and Technology Hellas
>
> www.exelixis-lab.org <http://www.exelixis-lab.org>
>
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP)
> lab,
> Institute of Molecular Biology and Biotechnology, Foundation for
> Research and Technology Hellas
>
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
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> To view this discussion on the web visit
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> --
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