ArticleiMeta2025
PhyloSuite v2: The development of an all-in-one, efficient and visualization-oriented suite for molecular dating analysis and other advanced features.
Article in iMeta, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed.
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- Reconstruction of an extinct soundscape reveals ultrasonic communication in the Jurassic.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Phylodynamic reconstruction of global evolution and geographic structure of maize chlorotic mottle virus.The Journal of general virology · 2026Article
- Mitogenomic Insights Into the Population Structure and Demographic History of Tree Shrews (Ecology and evolution · 2026Article
- Natural Selection Drives Codon Usage Bias in the Mitochondrial Genome ofAnimals : an open access journal from MDPI · 2026Article
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- A New Species of Eucnemidae (Coleoptera: Elateroidea) with Its Complete Mitogenome and Mitogenome-Based Phylogenetic Analysis.Biology · 2026Article
- Comparative Chloroplast Genome Analysis of Anchusa and the Adulterants of HERBA ANCHUSAE.Genes · 2026Article
- Hepatincolaceae (Alphaproteobacteria) Symbionts of Snapping ShrimpMicroorganisms · 2026Article
- Complete genome characterization, phylogenetic analysis, and capsid P2 variation of a goose astrovirus genotype 2 isolate from Guizhou, China.Poultry science · 2026Article
- A newInternational journal for parasitology. Parasites and wildlife · 2026Article
- The Complete Chloroplast Genome Sequences ofEcology and evolution · 2026Article
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- Deorphanization of the odorant receptor CsepOR1 identifies a biphasic behavioral modulator in Coccinella septempunctata (Coleoptera: Coccinellidae).Pest management science · 2026Article
- Calpains as Potential Regulators of Microtubule-Associated Cytokinesis: A Cross-Eukaryotic Unifying Hypothesis.Life (Basel, Switzerland) · 2026Article
- Assembly and comparative analysis of the complete mitochondrial genome of the endangered plant Fraxinus mandshurica.BMC plant biology · 2026Article
- Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MCMCtree and r8s are among the most popular molecular dating tools in the current genomic era, but their utility is hampered by steep learning curves, particularly concerning input file formatting, the complexity of fossil calibration setup, tree visualization, and model selection. To enhance their usability and improve research efficiency, we developed three new tools: MDGUI (for molecular dating analysis), TimeTreeAnno (for timetree visualization), and MCMCTracer (for convergence assessment). We integrated these into the PhyloSuite v2 platform, along with MCMCtree and r8s plugins, to create a comprehensive molecular dating suite. Compared to existing solutions that we benchmarked, our toolkit offers a more intuitive interface and streamlined workflow, featuring visual calibration point configuration, support for multiple alignment formats, automated model selection and implementation for downstream analyses, one-click pause/resume functionality, multithreading acceleration, and on-demand MCMC convergence assessment and plotting. Furthermore, PhyloSuite v2 introduces other advanced features, including gene duplicate resolution during the extraction step, significantly accelerated data handling capabilities (specifically, format conversion and concatenation), deeper integration of the latest IQ-TREE models and functions, and further streamlining of the entire phylogenetic analysis workflow. The update also includes adaptation to high-resolution screens and numerous bug fixes. The source code for the new version of PhyloSuite is available at https://github.com/dongzhang0725/PhyloSuite.
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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.