MOTIVATION The birth-death (BD) model constitutes the theoretical backbone of most phylogenetic tools for reconstructing speciation/extinction dynamics over time. Performing simulations of reconstructed trees (linking extant taxa) under the BD model in backward time, conditioned on the number of species sampled at present day and, in some cases, a specific time interval since the most recent common ancestor (MRCA), is needed for assessing the performance of reconstruction tools, for parametric bootstrapping and for detecting data outliers. The few simulation tools that exist scale poorly to large modern phylogenies, which can comprise thousands or even millions of tips (and rising). RESULTS Here I present efficient software for simulating reconstructed phylogenies under time-dependent BD models in backward time, conditioned on the number of sampled species and (optionally) on the time since the MRCA. On large trees, my software is 1000-10 000 times faster than existing tools. AVAILABILITY AND IMPLEMENTATION The presented software is incorporated into the R package 'castor', which is available on The Comprehensive R Archive Network (CRAN). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

中文翻译：

---

模拟数百万种树木。

动机出生死亡（BD）模型构成了大多数系统学工具的理论主干，这些工具可用于随着时间的推移重建物种/灭绝动力学。在BD模式下，根据当前采样的物种数量以及在某些情况下（自最近的共同祖先（MRCA）以来的特定时间间隔），对BD模型下的重建树木（链接现存分类群）进行模拟用于评估重建工具的性​​能，用于参数引导以及用于检测数据异常值。现有的少数模拟工具无法很好地缩放到大型现代系统发育，这些系统可能包含成千上万个（甚至不断增加）的技巧。结果在这里，我介绍了一种有效的软件，用于在时间依赖的BD模型下向后仿真模拟重建的系统发育，以采样物种的数量和（可选）自MRCA以来的时间为条件。在大树上，我的软件比现有工具快1000-10000倍。可用性和实施​​所提供的软件已集成到R包“ castor”中，该软件包可在The Composite R Archive Network（CRAN）上找到。补充信息补充数据可从Bioinformatics在线获得。