SH test

[Lixia Shi]

Dear professors,

    I have problems in doing SH test via Raxml in CIPRES.

    I have 13 trees inferred from 13 single mitochondrial genes,and I wanna compared them with a best tree separately, I know "-f h - t besttree.nwk -z 13trees.nwk", but I don't know the input sequence file after -s, each of the tree I put in has different sequence, should I put in the sequence of the best tree? 

     Thanks for your help!

[Alexandros Stamatakis]

in that case you can not compare the trees via the SH test, the
assumption is that all trees have been obtained from the very same
alignment!

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
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Lixia Shi]

Dear Prof.Alexis,

   Thank you so much for your reply. But I read a reference recently (the attachment), the author compared the topologies inferred from different sequence alignments. Would you mind having a look at this paper? 

   I really wnna do the same analyses with my datasets, so I ask you for help. Thanks a lot!

 Best,

Letitia.

在 2016年7月28日星期四 UTC+8下午4:38:48，Alexis写道：

[Alexandros Stamatakis]

why don't you ask the authors of the paper how they did the comparisons
exactly,

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
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology,
> University
> of Arizona at Tucson
>

> www.exelixis-lab.org <http://www.exelixis-lab.org>

[Lixia Shi]

yes Prof. Alexis, I asked the authors for help at first, but they just said them did this analysis on CIPRES, so I tried again and again on CIPRES (can not resolve it by myself), and then I went to the leader of CIPRES—Prof.Miller for help. At last, Prof.Miller told me you'll help me about this question~  

[Michael Weiß]

I guess what the authors did was to compare each of the best trees inferred from the partial datasets to the tree inferred from the "supergene" alignment. So the basis for all the SH tests should be this "supergene" dataset.

Kind regards, 

Michael

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Prof. Dr. Michael Weiß
http://bit.ly/17V8OJo (Google Scholar)
http://bit.ly/19OOusL (ResearchGate)
Researcher-ID: F-6206-2012
ORCID-ID: orcid.org/0000-0002-4869-9186 

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[Alexandros Stamatakis]

yes, that's very likely, thanks michael,

alexis

On 28.07.2016 12:02, Michael Weiß wrote:
> I guess what the authors did was to compare each of the best trees
> inferred from the partial datasets to the tree inferred from the
> "supergene" alignment. So the basis for all the SH tests should be this
> "supergene" dataset.
>
> Kind regards,
>
> Michael
> --
> Prof. Dr. Michael Weiß
> http://bit.ly/17V8OJo (Google Scholar)
> http://bit.ly/19OOusL (ResearchGate)
> Researcher-ID: F-6206-2012
> ORCID-ID: orcid.org/0000-0002-4869-9186

> <http://orcid.org/0000-0002-4869-9186>

>
>
>
>> Am 28.07.2016 um 11:57 schrieb 'Lixia Shi' via raxml

>> <ra...@googlegroups.com <mailto:ra...@googlegroups.com>>:

>> > www.exelixis-lab.org <http://www.exelixis-lab.org/>
>> <http://www.exelixis-lab.org <http://www.exelixis-lab.org/>>

>> >
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>> > You received this message because you are subscribed to the Google
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>> it, send
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>> > For more options, visit https://groups.google.com/d/optout
>> <https://groups.google.com/d/optout>.
>>
>> --
>> Alexandros (Alexis) Stamatakis
>>
>> Research Group Leader, Heidelberg Institute for Theoretical Studies
>> Full Professor, Dept. of Informatics, Karlsruhe Institute of
>> Technology
>> Adjunct Professor, Dept. of Ecology and Evolutionary Biology,
>> University
>> of Arizona at Tucson
>>

>> www.exelixis-lab.org <http://www.exelixis-lab.org/>

[Lixia Shi]

Dear Michael,

     Yes, you're right! I also put my "supergene" dataset in Raxml to be the basis, but I can't get the results I want, it seems that all my partial datasets are significant different from the “supergene” dataset. So I really don't know where the problems located.

      Thanks very much for your reply!

Best wishes,

Lixia.

[Lixia Shi]

Dear Prof.Alexis,

      Thanks a lot , I'll try again on CIPRES.

Best wishes,

Lixia.