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

Nhan Ly-Trong, Suha Naser-Khdour, Robert Lanfear, Bui Quang Minh*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    21 Citations (Scopus)


    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, and a comprehensive user tutorial at

    Original languageEnglish
    Article numbermsac092
    JournalMolecular Biology and Evolution
    Issue number5
    Publication statusPublished - 3 May 2022


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