Affiliation:
1. School of Computing, College of Engineering and Computer Science, Australian National University , Canberra, ACT 2600, Australia
2. Ecology and Evolution, Research School of Biology, College of Science, Australian National University , Canberra, ACT 2600, Australia
Abstract
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 1.4 h and 1.3 GB RAM to simulate alignments with one million sequences or sites, whereas popular software Seq-Gen, Dawg, and INDELible require 2–5 h and 50–500 GB of RAM. We provide AliSim as an extension of the IQ-TREE software version 2.2, freely available at www.iqtree.org, and a comprehensive user tutorial at http://www.iqtree.org/doc/AliSim.
Funder
Australian Research Council
Moore-Simons Foundation
Publisher
Oxford University Press (OUP)
Subject
Genetics,Molecular Biology,Ecology, Evolution, Behavior and Systematics
Cited by
26 articles.
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