Bootstrap trees

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Jul 12, 2021, 4:34:25 AMJul 12
to raxml

Hi all,
I have been using RAxML for more than a decade now. However, there is a question that I have not been able to get a proper answer regarding bootstrapping. What is the algorithm that is used to construct Bootstrap trees in each Bootstrap pseudoreplicate? This was not clearly stated in the manual when I checked the last time. I would appreciate if you could kindly explain this.


Alexandros Stamatakis

Jul 19, 2021, 12:09:47 AMJul 19
Dear Kanishka,

Sorry for the late reply, your message ended up in my SPAM folder.

If you are using RAxML-NG the new
version it's just the standard tree search algorithm of RAxML with some
slight modifications/improvements which are described in the PhD thesis
of Alexey Kozlov.

If you are using standard RAxML (not supported any more) and -f b RAxML
will apply it's standard search algorithm to the BS replicate. The
algorithm is described in the RAxML-VI and RAxML-III papers in

If you use -f x standard RAxML will use a faster more superficial
algorithm that is described in this paper here:

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Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP) lab,
Institute of Molecular Biology and Biotechnology, Foundation for
Research and Technology Hellas
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