use IQtree for ML searches

[shchurch]

IQtree may offer advantages to RAxML, GARLi. SOWHAT will need to read the required output from the results files (base freqs, transition rates, likelihood).

[vinjlynch]

Hi!

Any progress working IQtree into SOWHAT? I'd like to use SOWHAT on a binary character dataset, but neither RAxML nor GARLi implement the best-fitting model selected by ModelTest as implemented in IQtree (GTR2+FO+R3).

Thanks
Vinny

[shchurch]

Thanks for your interest, it's very helpful to know what folks are looking for / what would be most useful to implement. Unfortunately, no progress on this yet. While we are still hoping to incorporate IQtree, I think this would not fully solve the problem in this case, as the software for simulating new datasets (seq-gen) also does not offer that model as an option. Given that we would like to expand the set of models available for both inference and simulation, we have been considering other options. Will keep you posted if anything changes.

[vinjlynch]

Ah, forgot about that limitation of seq-gen. If you find a solution happy to share our dataset for testing. (And if anything comes of it include you as authors on any paper that uses the modified SOWHAT.)

Best,
Vinny