I'm working with 16S Sanger sequences and I want to do a phylogeny. I would like to know with which program I can get the substitution model of my sequences to later carry out my phylogeny in RAxML. Thank you.
The easiest thing would probably be to just build your tree in IQ-TREE, which has options to integrate the model selection and then build the tree using the selected model.
This can be done quite nicely in MEGA-X. Here you also get the prob. scores for the AIC and BIC and can select the best-fitting model accordingly
I use PartitionFinder2 (https://academic.oup.com/mbe/article/34/3/772/2738784). One helpful aspect is that you can set which models of evolution it should consider based on the program name that you plan on using for further analysis (e.g. BEAST, MrBayes).
I agree with Tyler Chafin ModelFinder implemented in IQ-TREE include the most up-to-date models of evolution for phylogenetic reconstruction. Alternatively, you could use jModelTest (http://evomics.org/learning/phylogenetics/jmodeltest/) before running RAxML.
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