Fwd: Query Regarding Species Tree for GeneRax

[Ankit Thakur]

Respected Sir,

I hope this email finds you well. My name is Ankit Thakur, and I am a PhD scholar in Computational Biology, CUHP. I have been using GeneRax for my research and greatly appreciate the tool’s contribution to phylogenetic analysis.

As I near the completion of my research, I am facing a challenge in reconciling the gene tree with the species tree. Specifically, I am uncertain about how to obtain or construct the species tree required by GeneRax. I would greatly appreciate any guidance you could provide on this matter.

Could you kindly suggest the best approach or recommended tools for generating a species tree that would be suitable for use in GeneRax? Any advice or references would be immensely helpful.

Thank you for your time and assistance. I look forward to your response.

Best regards,
Ankit Thakur
PhD Scholar CCBB Lab
CUHP, India

[Benoit Morel]

Dear Ankit Thakur,

Unfortunately there is no good answer for this question. The "best" species tree is the one that best matches the ground truth, and which tool to use is still an open research question.

GeneRax requires the species tree to be binary (which is the case for most species trees inferred with the standard methods) and rooted. Branch lengths don't matter.

I would either try with concatenation methods (raxml-ng for instance) or gene tree methods (astral, astral-pro, speciesrax)

Most of those methods output unrooted species trees. If you know the root position, you can root it manually. Otherwise you can try with speciesrax (which is actually part of the GeneRax tool).

Hope it helps.

Benoit 

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