raxml phylogeny with backbone tree

Developer Discussion
1

Good morning,

I’m writing because I would like to suggest adding a backbone flag option to qiime2 phylogeny raxml-rapid-bootstrap. This would allow the user to build the tree not from scratch, but using this reference backbone tree as the initial structure. I apologize if I missed this, but cannot find it in the documentation or the tutorials as implemented thus far.

Thanks in advance,

Camille

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3

Hi @camzdel,

This should be easy enough to add in the next update. Just to be clear, you are talking about the:

raxmlHPC -f t <user starting tree> ... flag correct?

I’ve created an issue here.

-Best wishes.
-Mike

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5

Thank you for your answer.

I am referring to Step 9 here: (constraint trees, backbone constraint): https://cme.h-its.org/exelixis/web/software/raxml/hands_on.html, which seems to be the [-r] flag: raxmlHPC-SSE3 -p12345 -r backboneConstraint.txt. This allows you to provide a backbone tree where the backbone tree sequences and new study sequences are aligned together in order to add the new sequences to this well-defined backbone constraint tree structure.

All the best,

Camille

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6

Ahh great! Thank you for clarifying this @camzdel! I’ll update the issue to reflect the topological constraint option. :hammer_and_wrench:

Meanwhile, I’d suggest q2-fragment-insertion.

-Mike

7

Thanks Mike,

q2-fragment-insertion could be a workaround, but ideally it would be great if this could be used with raxml to build trees. I hope you are able to add it as a flag in the next update-that would be amazing!

Best,

Camille

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