ArticleMolecular biology and evolution2022
AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era.
Article in Molecular biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53 citing papers in PubMed.
- Untangling the effects of within-host and between-host natural selection in viruses with applications to evolution of HIV-1 co-receptor usage.Journal of the Royal Society, Interface · 2026Article
- Evaluation of Molecular Phylogenetic Trees by an Information-Theoretic Metric.Journal of molecular evolution · 2026Article
- Molecular Clock Dating of Ancient Environmental DNA Reveals Damage Beyond Deamination.bioRxiv : the preprint server for biology · 2026Article
- GTRspmix: Capturing Heterogeneity of Exchangeabilities Across Sites to Improve Protein Phylogenetics.bioRxiv : the preprint server for biology · 2026Article
- Analysis of phylogenetic signal in protein language model embeddings.Scientific reports · 2026Article
- Article
- Algebraic Invariants for Inferring 4-Leaf Semi-Directed Phylogenetic Networks.Systematic biology · 2026Article
- Practical phylogenetic usage of theoretical advances in distance-based tree learning.BMC bioinformatics · 2026Article
- The heterogeneous selection landscape of genome evolution in prokaryotes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- IQ-TREE 3: phylogenomic inference software using complex evolutionary models.Molecular biology and evolution · 2026Article
- Cross-species prediction reveals chromatin regions with increased accessibility in humans.Science advances · 2026Article
- Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2.Nature biotechnology · 2026Article
- AliFilter: a machine learning approach to alignment filtering.Molecular biology and evolution · 2026Article
- Fast and accurate identification of emerging viral reassortment from genome sequences.Nucleic acids research · 2026Article
- Molecular clock dating using complex mixture models: applied to ancient symbionts.Molecular biology and evolution · 2026Article
- piqtree: a python package for seamless phylogenetic inference with IQ-TREE.Molecular biology and evolution · 2026Article
- Deep models of protein evolution in time generate realistic evolutionary trajectories and functional proteins.bioRxiv : the preprint server for biology · 2026Article
- RECUR: identifying recurrent amino acid substitutions from multiple sequence alignments.Molecular biology and evolution · 2026Article
- Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments Using AIC.Systematic biology · 2026Article
- Efficient algorithms for simulating sequences along a phylogenetic tree.Bioinformatics (Oxford, England) · 2026Article
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4 authors.
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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.
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