ArticleBioinformatics (Oxford, England)2023
AliSim-HPC: parallel sequence simulator for phylogenetics.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 16 citations in OpenAlex.
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- piqtree: a python package for seamless phylogenetic inference with IQ-TREE.Molecular biology and evolution · 2026Article
- RECUR: identifying recurrent amino acid substitutions from multiple sequence alignments.Molecular biology and evolution · 2026Article
- Unifying phylogenetic traversal and deep learning to guide tree exploration.bioRxiv : the preprint server for biology · 2026Article
- A timetree of Fungi dated with fossils and horizontal gene transfers.Nature ecology & evolution · 2025Article
- Accurate and Efficient Phylogenetic Inference through End-To-End Deep Learning.Molecular biology and evolution · 2025Article
- Accurate and Efficient Phylogenetic Inference through End-To-End Deep Learning.Molecular biology and evolution · 2025Article
- Ultrafast and ultralarge multiple sequence alignments using TWILIGHT.Bioinformatics (Oxford, England) · 2025Article
- Multiple merger coalescent inference of effective population size.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- nT4X and nT4M: Novel Time Non-reversible Mixture Amino Acid Substitution Models.Journal of molecular evolution · 2025Article
- CAT-Posterior Mean Site Frequencies Improves Phylogenetic Modeling Under Maximum Likelihood and Resolves Tardigrada as the Sister of Arthropoda Plus Onychophora.Genome biology and evolution · 2025Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 message passing interface (MPI) libraries, respectively. AliSim-HPC is highly efficient and scalable, which reduces the runtime to simulate 100 large gap-free alignments (30 000 sequences of one million sites) from over one day to 11 min using 256 CPU cores from a cluster with six computing nodes, a 153-fold speedup. While the OpenMP version can only simulate gap-free alignments, the MPI version supports insertion-deletion models like the sequential AliSim. AVAILABILITY AND IMPLEMENTATION: AliSim-HPC is open-source and available as part of the new IQ-TREE version v2.2.3 at https://github.com/iqtree/iqtree2/releases with a user manual at http://www.iqtree.org/doc/AliSim.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.