-m MFP = default?

[roblanf]

Discussed in https://github.com/orgs/iqtree/discussions/507

^{Originally posted by BjoernStelbrink December 18, 2025}
Dear all,

I am currently preparing a molecular phylogenetics course for our lab members, also including a tutorial on IQ-TREE 2. I came across the tip "Starting with version 1.5.4, -m MFP is the default behavior. Thus, this run is equivalent to iqtree -s example.phy" at https://iqtree.github.io/doc/Tutorial. I now noted, however, that both commands give different phylogenies and branch lengths, resulting from different best-fit models selected. So is that "tip" on the website not valid for IQ-TREE2?

Thank you and best wishes

Bjoern

[roblanf]

@claude what do you think of this?