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Substitution model selection in BEAST

I have constructed phylogenomic tree using the protein-coding genes of plant mitogenome using maximum likelihood method. Now I want to compare it using Bayesian method using BEAST.

The alignment file is amino acids instead of DNA.

  1. What is the best recommendation of substitution model to choose? The default is Blosum62
  2. Can I left other setting such as Trees, Operators, MCMC as default?
phylogenetic tree
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updated by Biodeer • Biodeer • written by wes • wes

1 answer

IQ-TREE's ModelFinder will help you find the substitution model that works best. There is also a paper if you wish to read the details.

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written by Mensur Dlakic Mensur Dlakic

Thanks Mensur Dlakic

The best-fit model according to AICc using ModelFinder is : HIVw+F+I+G4

However, may I know which substitution model should I choose as both BEAST version did not have HIVw option as shown in the printscreen below?

BEASTv.1.10.4 enter image description here

BEASTv.2.6.7 enter image description here

In addition, how to specify 'F' (empirical frequencies)? I only see empirical frequencies option if the HKY substitution model is chosen (nucleotide). However, my data type is amino acids.

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written by wes • wes

I don't use BEAST, so you may get better advice from someone else in that regard. It is quite possible that it doesn't have the HIVw matrix, in which case I suggest you go down the list of your best models until you find one that is implemented in BEAST. If you can't specify the fixed frequencies, the program will treat them probabilistically and will likely still find the best solution with maybe some extra work.

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written by Mensur Dlakic Mensur Dlakic

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