Guide tree for correcting topology

[Diego Soto Arancibia]

Hi everyone! I'm trying to become independent from CIPRES haha and learn to use RaxML through the command line in Ubuntu (inside WSL). I managed to run a pipeline to generate a tree from a concatenated matrix of five plant species genes, but I don't know how to add the partitions. How can this be done? Also, is it possible to add a guide tree generated by phylomaker to correct some of the topologies of the tree generated by raxml?

Thank you in advance!

[Alexandros Stamatakis]

Dear Diego,

> Hi everyone! I'm trying to become independent from CIPRES haha and learn
> to use RaxML through the command line in Ubuntu (inside WSL).

Great :-) are you using standard RAxML or RAxML-NG?

> I managed
> to run a pipeline to generate a tree from a concatenated matrix of five
> plant species genes, but I don't know how to add the partitions. How can
> this be done?

You need to use a partition file:

https://github.com/amkozlov/raxml-ng/wiki/Input-data#multiple-models

> Also, is it possible to add a guide tree generated by
> phylomaker to correct some of the topologies of the tree generated by raxml?

You can specify a constraint tree:

https://github.com/amkozlov/raxml-ng/wiki/Input-data#starting-trees

However, one may also interpret using a constraint as biasing the ML
tree inference. You absolutely need to check the ML scores of the
constrained tree search and compare them to the ML scores of the
unconstrained tree search as you might be imposing a tree structure by
using a constraint that is actually not supported by the data.

Alexis


>
> Thank you in advance!
>
>
>
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--
Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)