Comments (3)
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
from sowhat.
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.
from sowhat.
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
from sowhat.
Related Issues (20)
- Character dataset fails with newest RAxML HOT 2
- Add support for AUTO model specification in RAxML HOT 1
- Add tests with more intuitive messages for missing prerequisites HOT 1
- update documentation and usage subroutine to reflect RAxML default HOT 1
- seq-gen has limited model set. sowhat needs to check models before any processes are run. HOT 1
- Add more version information to sowhat.results HOT 1
- Possibly include stopping criterion HOT 1
- json output HOT 1
- instructions for monitoring a job - and cutting a job short HOT 1
- treetwo is better HOT 1
- sowhat should throw error if reps < 10 HOT 1
- add travis-ci integration
- add subroutine tests HOT 1
- include sowhat version in results.txt HOT 1
- mislabeled constrained / unconstrained values in report
- Failing travis ci due to old R HOT 4
- create docker image release HOT 1
- update and clean github documentation
- more obvious warning when not in sequential phylip HOT 1
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