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I'm running the Relax scan analysis. It seems like I always have different results using the same dataset and command line, also on the example data. I wonder if it is how it is suppose to be or there's something wrong with it.
Cheers
F
The text was updated successfully, but these errors were encountered:
Some of these analyses (including RELAX-scan) are quite noisy (complex models). The original README was test-run on a HyPhy release that is quite old and the new version has more stable and robust optimization routines.
If you run hyphy RELAX.bf --alignment data/Fig4H.nex with the current version you get
A better log likelihood (-1614.99 vs -1616.21) for the 2-rate model
The same two branches flagged as possibly relaxed/intensified and two new branches, which were marginal in the previous version
thanks a lot! What I'd to is run the regular RELAX on multiple subsequent branches and correct for multiple test afterward.
It's probably slower but more reliable I guess.
Hi @spond,
I'm running the Relax scan analysis. It seems like I always have different results using the same dataset and command line, also on the example data. I wonder if it is how it is suppose to be or there's something wrong with it.
Cheers
F
The text was updated successfully, but these errors were encountered: