Internode Certainty Verbose output

[Jacob Steenwyk]

Hi,

I was wondering if anyone has been able to run the verbose output of calculating internode certainty. Although I have appended the -C option, the output is the same as if the -C option were not present.

I am using RAxML version 8.2.10.

My command is the following:

raxmlHPC-PTHREADS -f i -t reference.tree -z set_of_trees.trees -m GTRCAT -n verbose.ic -C

The output I am getting are the newick trees with the lossless and probabilistic IC scores as well as the info file but I am not getting the output files detailing gene support frequencies and other information for each bipartition.

Any suggestions on what I may be doing wrong would be appreciated!

best,

Jacob

[Alexandros Stamatakis]

Hi Jacob,

I double-checked with a small example:

./raxmlHPC-AVX -f i -t RAxML_bestTree.ml -z RAxML_bootstrap.boot -m
GTRCAT -n verbose.ic -C

and get the following output files:

ls *.verbose.ic
RAxML_IC_Score_BranchLabels.verbose.ic RAxML_info.verbose.ic
RAxML_verboseSplits.verbose.ic

Maybe you should upgrade to v 8.2.11 and use the sequential version
instead of the PThreads version.

If you still don't get the verbose file then please send me the input
data to my personal email.

Alexis

On 10.04.2018 20:56, Jacob Steenwyk wrote:
> Hi Dr. Stamatakis,
>
> Thank you for your timely reply.
>
> The only files that are outputted include:
> RAxML_info.verbose.ic,
> RAxML_Corrected_Lossless_IC_Score_BranchLabels.verbose.ic,
> RAxML_Corrected_Probabilistic_IC_Score_BranchLabels.verbose.ic
>
> I do not see the file you described. It superficially seems as if the -C
> parameter is not recognized.
>
> best,
>
> Jacob
>
> On Tue, Apr 10, 2018 at 1:06 PM, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>> wrote:
>
> Is there nothing printed to a file called:
>
> RAxML_verboseIC.verbose.ic ?
>
> 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
>
> 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

www.exelixis-lab.org

[Alexis]

Hi Jacob,

Just checked the data you sent me. The reason why you don't get verbose output can be found in the terminal output: 

The trees in tree set don't have the same size, executing IC/TC algorithm with correction ... 

Meaning that your input tree have partially less taxa than the reference tree, that's why RAxML switches to a different algorithm that is also described in a different paper:

https://academic.oup.com/mbe/article/33/6/1606/2579777

This algorithm does not have verbose output as it is pretty different from the other one. 

If you are looking for something more recent for partial gene trees you can try this new method here: 

https://www.biorxiv.org/content/early/2017/07/27/168526

Alexis

> <alexandros.stamatakis@gmail.com

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[Jacob Steenwyk]

Thank you very much for your quick reply. Thank you!

best,

Jacob

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