3 votes
Accepted

Should I expect / use a prokaryote-specific substitution model when building a phylogenetic tree?

IQTree is a fashionable method for speeding up bootstrapping and used on ultra large datasets. What IQTree might be doing is rigidly fixing a model and parameterisation is not estimate via the ML. ...
M__'s user avatar
  • 12.1k
3 votes
Accepted

File format of substitution matrix in clustalw

This example seems to have information on this, looks like it should have this format: ...
Bioinfomrat's user avatar

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