Open francicco opened 1 year ago
Dear @francicco,
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
Branch | Previous p | Current p | k (old/new) |
---|---|---|---|
Node 7 | 0.04 | 0.04 | 0 / 0.10 |
EU912347 ... | 0.00 | 0.00 | 0.10 / 0.07 |
EU912347 ... | 0.00 | 0.00 | 0.10 / 0.07 |
Node7 | 0.12 | 0.04 | 0.21 / 0.10 |
EU912349 | 0.09 | 0.01 | 0.22 / 0.11 |
Best, Sergei
Hi Sergei,
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.
Cheers F
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