As genomic sequence data becomes increasingly available, inferring the phylogeny of the species as that of concatenated genomic data can be enticing. However, this approach makes for a biased estimator of branch lengths and substitution rates and an inconsistent estimator of tree topology. Bayesian multispecies coalescent methods address these issues. This is achieved by constraining a set of gene trees within a species tree and jointly inferring both under a Bayesian framework. However, this approach comes at the cost of increased computational demand. Here, we introduce StarBeast3 – a software package for efficient Bayesian inference under the multispecies coalescent model via Markov chain Monte Carlo. We gain efficiency by introducing cutting-edge proposal kernels and adaptive operators, and StarBeast3 is particularly efficient when a relaxed clock model is applied. Furthermore, gene tree inference is parallelised, allowing the software to scale with the size of the problem. We validated our software and benchmarked its performance using three real and two synthetic datasets. Our results indicate that StarBeast3 is up to one-and-a-half orders of magnitude faster than StarBeast2, and therefore more than two orders faster than *BEAST, depending on the dataset and on the parameter, and can achieve convergence on large datasets with hundreds of genes. StarBeast3 is open-source and is easy to set up with a friendly graphical user interface.

中文翻译：

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StarBeast3：多物种合并下的自适应并行贝叶斯推理

随着基因组序列数据变得越来越可用，将物种的系统发育推断为串联基因组数据的系统发育可能很诱人。然而，这种方法会导致对分支长度和替换率的估计有偏差，并且对树拓扑的估计会不一致。贝叶斯多物种聚结方法解决了这些问题。这是通过将一组基因树限制在物种树内并在贝叶斯框架下共同推断两者来实现的。然而，这种方法是以增加计算需求为代价的。在这里，我们介绍 StarBeast3——一个通过马尔可夫链蒙特卡罗在多物种聚结模型下进行高效贝叶斯推理的软件包。我们通过引入尖端的提案内核和自适应算子来提高效率，而 StarBeast3 在应用宽松时钟模型时特别有效。此外，基因树推理是并行的，允许软件随问题的大小进行扩展。我们使用三个真实数据集和两个合成数据集验证了我们的软件并对其性能进行了基准测试。我们的结果表明，StarBeast3 比 StarBeast2 快一个半数量级，因此比 *BEAST 快两个数量级以上，具体取决于数据集和参数，并且可以在大型数据集上实现收敛数百个基因。StarBeast3 是开源的，易于设置，具有友好的图形用户界面。我们使用三个真实数据集和两个合成数据集验证了我们的软件并对其性能进行了基准测试。我们的结果表明，StarBeast3 比 StarBeast2 快一个半数量级，因此比 *BEAST 快两个数量级以上，具体取决于数据集和参数，并且可以在大型数据集上实现收敛数百个基因。StarBeast3 是开源的，易于设置，具有友好的图形用户界面。我们使用三个真实数据集和两个合成数据集验证了我们的软件并对其性能进行了基准测试。我们的结果表明，StarBeast3 比 StarBeast2 快一个半数量级，因此比 *BEAST 快两个数量级以上，具体取决于数据集和参数，并且可以在大型数据集上实现收敛数百个基因。StarBeast3 是开源的，易于设置，具有友好的图形用户界面。