Can the SH test be used on Newick files giving topology only?

[Rachel Rodgers]

Hi all,

When running the SH-test in RAxML, should you pass in trees as they are formatted after a RAxML search, or can you run the test on tree files that show topology only?  I have done both approaches and the results are vastly different. 

For example, the format produced by RAxML looks like:

((((((F._zebrinus:0.01525720481483303602,(A._xenica:0.02079484906893935489,(((F._nottii:0.00638980204047356198,F._chrysotus:0.01123931779044414631):0.00831283555904896790,(F._olivaceus:0.00376560650291416291,F._notatus:0.00542664988626936212):0.00844307750421485585):0.00081826736513124004,F._sciadicus:0.01589004759583248841):0.00072408581858648491):0.00081844567460135416):0.00131693030480839945,F._similis:0.02126637967059911982):0.00054404536578163095,(((F._diaphanus:0.00476846485758310699,F._rathbuni:0.00368104869859165081):0.00398517481373079560,F._catenatus:0.00792200736276942041):0.00105708322838712378,(F._heteroclitus:0.00994130042501269878,F._grandis:0.00451465440676790657):0.00745618299455668657):0.00273609083183778707):0.00338464022846559709,(L._goodei:0.00581592710316395332,L._parva:0.00499310546584902978):0.02944257321239649242):0.00611420133153332997,F._parvipinnis:0.02290288688562440791):0.02277402275785951266,(C._variegatus:0.10189323765343578920,(O._latipes:0.32562542362622071135,(X._maculatus:0.02641194359801729216,P._reticulata:0.02695217980079970058):0.04691276262911108635):0.00828028949621204338):0.02277402275785951266);

but a topology-only file would look like:

((((((F._zebrinus,((F._chrysotus,A._xenica),((F._nottii,(F._olivaceus,F._notatus)),F._sciadicus))),F._similis),(((F._diaphanus,F._rathbuni),F._catenatus),(F._heteroclitus,F._grandis))),(L._goodei,L._parva)),F._parvipinnis),(C._variegatus,(O._latipes,(X._maculatus,P._reticulata))));

I'm assuming that the first format is the appropriate one since it's the data generated by RAxML.  (After all, the second format is what I used to start an ML search for a constrain tree.)  Or so I think?

Thanks,

Rachel

[Alexandros Stamatakis]

you should be able to do both, as long as you pass Newick-formatted
trees ... in which sense are the results vastly different?

alexis

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[Rachel Rodgers]

Sorry for such a long delay...I wasn't getting notified when I got a response and completely forgot.  I was getting very different likelihood scores for the same tree depending on which format of that tree I input into RAxML, thus changing the results of the SH-test.  I ended up sticking with the outputs that were generated directly from the ML search, it just makes more sense I guess.

Thank you!

Rachel

[Alexandros Stamatakis]

can you maybe nonetheless send me the command line you used?

thanks,

alexis

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

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

[Rachel Rodgers]

Yes, I will try to get that to you, thanks! 

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of Arizona at Tucson

www.exelixis-lab.org

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[Rachel Rodgers]

Sorry, I'm not good at replying very quickly.

I am attaching the .info files that were recorded when I ran these processes.  Each command only had two trees - the best unconstrained tree and one constraint tree.  The file starting with RAXML_DIRECT_OUTPUT was the run that used trees in the format in which they were directly output from RAxML (with the numbers recorded into the tree file).  The one called TOPOLOGY_ONLY was, of course, the run using trees with only the topology specified in the file. 

Sorry for the confusing commands.  They are the same commands, just out of order.  I am a terrible human when it comes to digital organization.

I'm hoping to submit an article for publication soon, so hopefully I have run the test correctly, but want to fix it if I screwed it up.  Again, I went with the results which used trees formatted as they were output from RAxML.

Thanks so much.

[Alexandros Stamatakis]

could you please send me the tree files, my guess is that the tree
topologies of the constrained trees passed via -z might just be
different, you can also check this yourself by computing the RF distance
between the two constrained input trees ...

alexis

[Rachel Rodgers]

Sure, here you go.  I renamed them a bit to make it easier.  Thank you!

Rachel

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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

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[Alexandros Stamatakis]

dear rachel,

the two constrained trees you sent have different topologies, hence they
should yield different likelihoods, which they actually do :-)

alexis

On 22.05.2017 22:29, Rachel Rodgers wrote:
> Sure, here you go. I renamed them a bit to make it easier. Thank you!
>
> Rachel
>
> On Mon, May 22, 2017 at 2:56 PM, Alexandros Stamatakis
> <alexandros...@gmail.com

> <mailto:raxml%2Bun...@googlegroups.com> <javascript:>
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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>
> <http://www.exelixis-lab.org>
>
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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>
>
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[Rachel Rodgers]

Thanks, I'll have to look at that, I don't know why that would be. I fed that constraint topology to RAxML to get the other tree.

Rachel 

On May 23, 2017 12:07 AM, "Alexandros Stamatakis" <alexandros...@gmail.com> wrote:

dear rachel,

the two constrained trees you sent have different topologies, hence they should yield different likelihoods, which they actually do :-)

alexis

On 22.05.2017 22:29, Rachel Rodgers wrote:

Sure, here you go.  I renamed them a bit to make it easier.  Thank you!

Rachel

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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>

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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

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[Rachel Rodgers]

I see now, THAT was stupid of me.  No clue how that happened but at least I have time to fix it.  Thanks again!

On Tue, May 23, 2017 at 9:12 AM, Rachel Rodgers <rachelr...@gmail.com> wrote:

Thanks, I'll have to look at that, I don't know why that would be. I fed that constraint topology to RAxML to get the other tree.

Rachel