prior(PriorType.CTMC_RATE_REFERENCE_PRIOR).initial(rate)
<BUG>.isCMTCRate(true).isNonNegative(true).partitionOptions(this).build(parameters);
new Parameter.Builder(ClockType.UCLD_MEAN, "uncorrelated lognormal relaxed clock mean").</BUG>
prior(PriorType.CTMC_RATE_REFERENCE_PRIOR).initial(rate)
<BUG>.isCMTCRate(true).isNonNegative(true).partitionOptions(this).build(parameters);
new Parameter.Builder(ClockType.UCGD_MEAN, "uncorrelated gamma relaxed clock mean").</BUG>
prior(PriorType.CTMC_RATE_REFERENCE_PRIOR).initial(rate)
<BUG>.isCMTCRate(true).isNonNegative(true).partitionOptions(this).build(parameters);
} else {</BUG>
new Parameter.Builder("clock.rate", "substitution rate").

prior(PriorType.CTMC_RATE_REFERENCE_PRIOR).initial(rate)
.isCMTCRate(true).isNonNegative(true).partitionOptions(this)
.isAdaptiveMultivariateCompatible(true).build(parameters);
new Parameter.Builder(ClockType.UCLD_MEAN, "uncorrelated lognormal relaxed clock mean").
prior(PriorType.CTMC_RATE_REFERENCE_PRIOR).initial(rate)
.isCMTCRate(true).isNonNegative(true).partitionOptions(this)
.isAdaptiveMultivariateCompatible(true).build(parameters);
new Parameter.Builder(ClockType.UCGD_MEAN, "uncorrelated gamma relaxed clock mean").
prior(PriorType.CTMC_RATE_REFERENCE_PRIOR).initial(rate)
.isCMTCRate(true).isNonNegative(true).partitionOptions(this)
.isAdaptiveMultivariateCompatible(true).build(parameters);
} else {
new Parameter.Builder("clock.rate", "substitution rate").
