: This is the seminal paper assessing the code quality and software engineering practices of major tools in the field, including Java-based tools like BEAST . It highlights the need for better software quality to ensure scientific reproducibility. Read the full paper on bioRxiv
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Engine<DoubleGene, Double> engine = Engine.builder(problem) .populationSize(500) .survivorsSelector(new TournamentSelector<>(3)) .alterers(new Mutator<>(0.1), new Crossover<>(0.8)) .build(); The State of Software for Evolutionary Biology :
EvolutionResult<DoubleGene, Double> result = engine.stream() .limit(100) .collect(EvolutionResult.toBestEvolutionResult()); (3)) .alterers(new Mutator<
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