Ly-Trong, N. | bioRxiv Science

bioRxiv2023

AliSim-HPC: parallel sequence simulator for phylogenetics

MotivationSequence simulation plays a vital role in phylogenetics with many applications, such as evaluating phylogenetic methods, testing hypotheses, and generating training data for machine-learning applications. We recently introduced a new simulator for multiple sequence alignments called AliSim, which outperformed existing tools. However, with the increasing demands of simulating large data sets, AliSim is still slow due to its sequential implementation; for example, to simulate millions of sequence alignments, AliSim took several days or weeks. Parallelization has been used for many phylogenetic inference methods but not yet for sequence simulation. ResultsThis paper introduces AliSim-HPC, which, for the first time, employs high-performance computing for phylogenetic simulations. AliSim-HPC parallelizes the simulation process at both multi-core and multi-CPU levels using the OpenMP and MPI libraries, respectively. AliSim-HPC is highly efficient and scalable, which reduces the runtime to simulate 100 large alignments from one day to 9 minutes using 256 CPU cores from a cluster with 6 computing nodes, a 162-fold speedup. Availability and implementationAliSim-HPC is open source and available as part of the new IQ-TREE version v2.2.2.2 at https://github.com/iqtree/iqtree2/releases with a user manual at http://www.iqtree.org/doc/AliSim. Contactm.bui@anu.edu.au

evolutionary biology↗

bioRxiv2021

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

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 programs exist, but the most feature-rich programs tend to be rather slow, and the fastest programs 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 approach. AliSim takes 1.3 hours and 1.3 GB RAM to simulate alignments with one million sequences or sites, while popular software Seq-Gen, Dawg, and INDELible require two to five hours and 50 to 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.

bioinformatics↗