SH test

Maryam Nadimi

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Nov 23, 2015, 2:27:58 PM11/23/15

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Hi,

I have a question regarding Sh test via -f. I know I need to use -z and -t but I don't know how to use the. Let say I have tree (A) and tree (B), and so I have the FASTA file of their alignments already uploaded in Cipres to get the trees by RAxML, what do I need to upload and select for -t and -z.

Thanks,

Terri

William Gearty

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Nov 23, 2015, 2:37:49 PM11/23/15

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This seems more relevant to the CIPRES google group:
https://groups.google.com/forum/#!forum/cipres-science-gateway-users

Also, both of those options should be available in the RAxML on XSEDE parameters (advanced parameters).

-Will

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William Gearty

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Alexandros Stamatakis

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Nov 23, 2015, 2:49:56 PM11/23/15

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-t is the best-scoring ML tree, -z contains the tree/trees you want to
test against that have a worse ML score,

alexis

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Alexandros (Alexis) Stamatakis

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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

Maryam Nadimi

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Nov 23, 2015, 3:11:01 PM11/23/15

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Thanks Alexis. So if I have t2o trees to be compared I need to use one in newick format in it and another one in -t again in newick format! Am I right?

Best,

Alexandros Stamatakis

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Nov 23, 2015, 3:12:06 PM11/23/15

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that's right,

alexis

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> Alexandros (Alexis) Stamatakis
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> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
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> www.exelixis-lab.org <http://www.exelixis-lab.org>

Maryam Nadimi

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Nov 23, 2015, 3:13:56 PM11/23/15

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Thanks Alexis. So if I have two trees to be compared I need to use one in newick format in -t and another one in -z again in newick format! Am I right?

Best,

Maryam Nadimi

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Nov 23, 2015, 3:15:49 PM11/23/15

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Thanks William. i don't know why I am not able to post in CIPRES group!

Maryam Nadimi

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Nov 23, 2015, 3:17:17 PM11/23/15

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Thanks Alexis.

And what shall ai choose for data then to run this task?

William Gearty

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Nov 23, 2015, 3:17:21 PM11/23/15

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Are you a member?

There might be an approval process, not sure.

Maryam Nadimi

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Nov 23, 2015, 3:23:19 PM11/23/15

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I supposed to be a member :) I'll check.

Thanks anyway,

Alexandros Stamatakis

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Nov 24, 2015, 3:18:47 AM11/24/15

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you mean in terms of alignment?

just the alignment on which you inferred the tree.

alexis

Maryam Nadimi

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Nov 25, 2015, 10:06:59 AM11/25/15

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I know Alexis, But since I am going to compare 2 trees that I need to use them via -z and -t then what alignment I should use for the data that I wan to run the task? Shall I use just one of them (alignment) for the data?

Best,

Mary

Alexandros Stamatakis

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Nov 26, 2015, 12:36:01 PM11/26/15

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well you can only compare trees with all those statistical tests that
have been inferred on exactly the same data/alignment, otherwise you
can't compare likelihoods anyway,

alexis

Lixia Shi

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Jul 27, 2016, 10:57:31 PM7/27/16

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Hi Alexis,

You mean if I have trees inferred on different alignment, I can't compare their likelihoods with one best tree separately?

Lixia Shi

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Jul 27, 2016, 11:03:38 PM7/27/16

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Dear Maryam Nadimi,

Have you solved your problem? I have the same trouble now in doing SH test via Raxml,

cuz my trees were inferred from different sequence alignments, I don't know which file to put after -s,

do you know now? Could you please tell me if you know already? Thank you !

Alexandros Stamatakis

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Jul 28, 2016, 4:39:58 AM7/28/16

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On 28.07.2016 04:57, 'Lixia Shi' via raxml wrote:
> Hi Alexis,
> * You mean if I have trees inferred on different alignment, I can't

> compare their likelihoods with one best tree separately?

yes, and actually this is a theoretical issue not a practical one, you
can only compare likelihoods for estimates obtained from the same data!

alexis

> *

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