Jariani Abbas, Warth Christopher, Deforche Koen, Libin Pieter, Drummond Alexei J, Rambaut Andrew, Matsen Iv Frederick A, Theys Kristof
Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.
Laboratory for Systems Biology, VIB, Leuven, Belgium.
Virus Evol. 2019 Mar 8;5(1):vez003. doi: 10.1093/ve/vez003. eCollection 2019 Jan.
Simulations are widely used to provide expectations and predictive distributions under known conditions against which to compare empirical data. Such simulations are also invaluable for testing and comparing the behaviour and power of inference methods. We describe SANTA-SIM, a software package to simulate the evolution of a population of gene sequences forwards through time. It models the underlying biological processes as discrete components: replication, recombination, point mutations, insertion-deletions, and selection under various fitness models and population size dynamics. The software is designed to be intuitive to work with for a wide range of users and executable in a cross-platform manner.
模拟被广泛用于在已知条件下提供期望值和预测分布，以便与实证数据进行比较。此类模拟对于测试和比较推理方法的行为及功效也非常宝贵。我们描述了SANTA-SIM，这是一个用于模拟基因序列群体随时间向前演化的软件包。它将潜在的生物学过程建模为离散组件：复制、重组、点突变、插入缺失，以及在各种适应度模型和种群大小动态下的选择。该软件设计得让广泛的用户易于使用，并且能够以跨平台的方式执行。
