AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era.

ABSTRACT: Sequence simulators play an important role in phylogenetics. Simulated data has many applications, such as evaluating the performance of different methods, hypothesis testing with parametric bootstraps, and, more recently, generating data for training machine-learning applications. Many sequence simulation programmes exist, but the most feature-rich programmes tend to be rather slow, and the fastest programmes tend to be feature-poor. Here, we introduce AliSim, a new tool that can efficiently simulate biologically realistic alignments under a large range of complex evolutionary models. To achieve high performance across a wide range of simulation conditions, AliSim implements an adaptive approach that combines the commonly used rate matrix and probability matrix approaches. AliSim takes 1.

SUBMITTER: Ly-Trong N 

PROVIDER: S-EPMC9113491 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature