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MutableAlignment

Alignments that can change during MCMC for BEAST 3.

Maven coordinates

<dependency>
    <groupId>io.github.compevol</groupId>
    <artifactId>mutable-alignment</artifactId>
    <version>0.1.0-SNAPSHOT</version>
</dependency>

JPMS module: mutable.alignment

API

Replace the standard Alignment with mutablealignment.MutableAlignment and TreeLikelihood with mutablealignment.MATreeLikelihood.

The MutableAlignment can be changed by operators using:

  • setSiteValue() — set a single character in the alignment
  • setSiteValuesByTaxon() — set a sequence for a taxon
  • setSiteValuesBySite() — set site values for all taxa (single site)
  • setSiteValues() — set the whole alignment

Note that setSiteValue() and setSiteValuesByTaxon() are inefficiently implemented: partials will be recalculated for all sites. A future BEAGLE-aware implementation will probably suffer from the same limitation due to the BEAGLE API not allowing efficient updates of single sites.