INQUIRY ON RAXML-NG CONSENSUS TREE OPTIONS

[Jeremiah Sia]

Hi, 

Good day,

I have ran my analysis on RAxML-NG but i cant seem to confirm whether the consensus tree was generated from majority rule or strict consensus, I have looked through the output files, so far, i cant find any information. May i know which of the consensus tree options were used for the analysis? When I was setting the parameters, the options were blocked out from selection. Please advise. 

Thank you. 

Regards,

Jeremiah

[Pfeiffer, Wayne]

Hi Jeremiah,

The -consense option of RAxML-NG is not exposed in the version of RAxML-NG available via CIPRES.

The all-in-one analysis that you ran did 20 maximum likelihood searches starting from different initial trees and output the tree with the best ML score in infile.txt.raxml.bestTree. This tree also contains the support values obtained from 900 bootstrap searches.

Consensus trees of two groups of bootstrap trees are computed as part of the autoMRE bootstrapping test, but the consensus trees are not output.

Best regards,

Wayne

On Feb 16, 2026, at 5:48 PM, Jeremiah Sia <jerem...@gmail.com> wrote:

Hi Arshad and Wayne,

Thank you for your reply. Please refer to the attached files.

Thanks.

Regards,

Jeremiah 

On Tue, 17 Feb 2026, 08:19 Pfeiffer, Wayne, <pfei...@sdsc.edu> wrote:

Hi Jeremiah,

* Please send us your _JOBINFO.TXT file.

Thanks,

Wayne

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[Jeremiah Sia]

Dear Wayne,

Good day.

Understood and thank you for your explanation. 

Regards,

Jeremiah