Related Issues (20)
- `phydms_logoplot` does not create new output directory
- underflow error with HIV and `--brlen optimize` HOT 3
- `--diffprefsbysite` does **not** work with `--gammaomega` HOT 1
- examples of `YNGKP_M0` *not* optimizing HOT 5
- `scipy` convergence but Jacobian still large HOT 3
- Q values should be for one sided tests? HOT 1
- DMS2_batch_prefs MCMC does not converge on certain ENV sites HOT 1
- incompatibile with `pandas` 0.25 HOT 1
- `phydms_prepalignment` protein dictionary key error HOT 3
- FloatingPointError: divide by zero encountered in true_divide HOT 11
- change `scipy.XXX` to `numpy.XXX` for `scipy 2.0.0` deprecation warning
- Sites in ExpCM preferences file must start with 1? HOT 1
- phydms_plotselection HOT 3
- list index out of range in phydms_prepalignments HOT 1
- Can phydms calculate dN/dS ratios for entire genes in phylogeny? HOT 1
- some tweaks to phydms_testdivpressure
- check `divPressureValues` in `ExpCM_empirical_phi_divpressure` HOT 1
- Underflow error with `YNGKP_M5` HOT 3
- `--brlen` does not accept "fix" as an argument HOT 1
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