how to compare the topology similarity between full tree and subsampled trees?

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Brandon Stark

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Jun 2, 2022, 10:36:07 PM6/2/22
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I want to  compare the topology similarity between full tree and subsampled trees from full datasets and 3 subsampled datasets, how to analysis it, thanks.

Alexandros Stamatakis

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Jun 3, 2022, 3:44:06 AM6/3/22
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Maybe the attached book chapter describes what you need.

This plausibility algorithm calculates exactly what you need I believe
and is implemented in standard RAxML:

https://github.com/stamatak/standard-RAxML

Alexis
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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
Chapter 34 (Dao et al.).pdf

Brandon Stark

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Jul 16, 2022, 11:58:15 PM7/16/22
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sorry, i can not find of it, can you help me figure it out, thanks.

Alexandros Stamatakis

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Jul 17, 2022, 11:56:31 PM7/17/22
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What exactly are you not able to find?

Alexis

On 17.07.22 06:58, Brandon Stark wrote:
> sorry, i can not find of it, can you help me figure it out, thanks.
>
> 在2022年6月3日星期五 UTC+8 15:44:06<Alexis> 写道:
>
> Maybe the attached book chapter describes what you need.
>
> This plausibility algorithm calculates exactly what you need I believe
> and is implemented in standard RAxML:
>
> https://github.com/stamatak/standard-RAxML
> <https://github.com/stamatak/standard-RAxML>
>
> Alexis
>
> On 03.06.22 05:36, Brandon Stark wrote:
> > I want to  compare the topology similarity between full tree and
> > subsampled trees from full datasets and 3 subsampled datasets,
> how to
> > analysis it, thanks.
> >
> > --
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> > Groups "raxml" group.
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> send
> > an email to raxml+un...@googlegroups.com
> > <mailto:raxml+un...@googlegroups.com>.
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> >
> https://groups.google.com/d/msgid/raxml/f95abdba-8e40-4ee4-a1ce-30923e159dddn%40googlegroups.com
> <https://groups.google.com/d/msgid/raxml/f95abdba-8e40-4ee4-a1ce-30923e159dddn%40googlegroups.com>
>
> >
> <https://groups.google.com/d/msgid/raxml/f95abdba-8e40-4ee4-a1ce-30923e159dddn%40googlegroups.com?utm_medium=email&utm_source=footer
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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 <http://www.exelixis-lab.org>
>
> --
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