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Looking for some suggestions - I'm working with Archaeal genomic regions whose optimally fitting model seems to be Tamura-Nei (https://doi.org/10.1093/oxfordjournals.molbev.a040023).

Would it be too much to suspect the Archaeal region is under similar types of evolutionary pressure?

#archaea #microbiology #evolution #phylogenetics #bioinformatics

#Evolution #bioinformatics #microbiology #archaea #phylogenetics
in reply to naturepoker

Frank Aylward
Frank Aylward
• •
seems reasonable. Are you thinking there is a bias towards some substitutions?
in reply to Frank Aylward

naturepoker
naturepoker
• •
@foaylward yes - though I'm wondering if I'm looking at a very happenstance mathematical match, more so than anything biologically meaningful
@Frank Aylward
in reply to naturepoker

Frank Aylward
Frank Aylward
• •
if it's just model fit with something like Iqtree I would follow up with something more specific, or look at the difference with the next best model.
in reply to Frank Aylward

grimmiges
grimmiges
• •

@foaylward
With the speediness of the current ML tools, why not just take a data set and run it using the plethora of models, including fully customised ones in RAxML-ng, and just test, if there's any critical effect on the topology by e.g. comparing the ML-BS supports across models for the same splits.

Screenshot from https://github.com/amkozlov/raxml-ng/wiki/Input-data

Input data

RAxML Next Generation: faster, easier-to-use and more flexible - amkozlov/raxml-ng
GitHub
@Frank Aylward

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