{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T11:03:09Z","timestamp":1774263789669,"version":"3.50.1"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T00:00:00Z","timestamp":1693526400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014989","name":"Chan-Zuckerberg Initiative","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100014989","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Sequence 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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>This 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\u2009000 sequences of one million sites) from over one day to 11\u2009min 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\u2013deletion models like the sequential AliSim.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad540","type":"journal-article","created":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T19:55:02Z","timestamp":1693598102000},"source":"Crossref","is-referenced-by-count":16,"title":["AliSim-HPC: parallel sequence simulator for phylogenetics"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5668-5027","authenticated-orcid":false,"given":"Nhan","family":"Ly-Trong","sequence":"first","affiliation":[{"name":"School of Computing, College of Engineering, Computing and Cybernetics, Australian National University , Canberra, ACT 2600, Australia"}]},{"given":"Giuseppe M J","family":"Barca","sequence":"additional","affiliation":[{"name":"School of Computing, College of Engineering, Computing and Cybernetics, Australian National University , Canberra, ACT 2600, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5535-6560","authenticated-orcid":false,"given":"Bui Quang","family":"Minh","sequence":"additional","affiliation":[{"name":"School of Computing, College of Engineering, Computing and Cybernetics, Australian National University , Canberra, ACT 2600, Australia"}]}],"member":"286","published-online":{"date-parts":[[2023,9,1]]},"reference":[{"key":"2023092805224284000_btad540-B1","doi-asserted-by":"crossref","first-page":"3338","DOI":"10.1093\/molbev\/msaa154","article-title":"ModelTeller: model selection for optimal phylogenetic reconstruction using machine learning","volume":"37","author":"Abadi","year":"2020","journal-title":"Mol Biol Evol"},{"key":"2023092805224284000_btad540-B2","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1007\/BF00176093","article-title":"Monte Carlo simulation in phylogenies: an application to test the constancy of evolutionary rates","volume":"38","author":"Adell","year":"1994","journal-title":"J Mol Evol"},{"key":"2023092805224284000_btad540-B3","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1093\/bioinformatics\/btg427","article-title":"Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference","volume":"20","author":"Altekar","year":"2004","journal-title":"Bioinformatics"},{"key":"2023092805224284000_btad540-B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pcbi.1003537","article-title":"BEAST 2: a software platform for Bayesian evolutionary analysis","volume":"10","author":"Bouckaert","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"2023092805224284000_btad540-B5","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/B978-0-12-804189-5.00002-8","volume-title":"Embedded Computing for High Performance","author":"Cardoso","year":"2017"},{"key":"2023092805224284000_btad540-B6","doi-asserted-by":"crossref","first-page":"iii31","DOI":"10.1093\/bioinformatics\/bti1200","article-title":"DNA assembly with gaps (Dawg): simulating sequence evolution","volume":"21","author":"Cartwright","year":"2005","journal-title":"Bioinformatics"},{"key":"2023092805224284000_btad540-B7","volume-title":"Using OpenMP: Portable Shared Memory Parallel Programming (Scientific and Engineering Computation)","author":"Chapman","year":"2007"},{"key":"2023092805224284000_btad540-B8","doi-asserted-by":"crossref","first-page":"e1010056","DOI":"10.1371\/journal.pcbi.1010056","article-title":"phastSim: efficient simulation of sequence evolution for pandemic-scale datasets","volume":"18","author":"De Maio","year":"2022","journal-title":"PLoS Comput Biol"},{"key":"2023092805224284000_btad540-B9","volume-title":"Inferring Phylogenies","author":"Felsenstein","year":"2004"},{"key":"2023092805224284000_btad540-B10","doi-asserted-by":"crossref","first-page":"1879","DOI":"10.1093\/molbev\/msp098","article-title":"INDELible: a flexible simulator of biological sequence evolution","volume":"26","author":"Fletcher","year":"2009","journal-title":"Mol Biol Evol"},{"key":"2023092805224284000_btad540-B11","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1093\/sysbio\/42.3.265","article-title":"Phylogenetic analysis of covariance by computer simulation","volume":"42","author":"Garland","year":"1993","journal-title":"Syst. 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