ArticleBioinformatics advances2023
Phylostems: a new graphical tool to investigate temporal signal of heterochronous sequences datasets.
Article in Bioinformatics advances, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Article
- Tracing the evolutionary trajectory of Japanese encephalitis virus across hosts and countries.Scientific reports · 2025Article
- Diversification of an emerging bacterial plant pathogen; insights into the global spread of Xanthomonas euvesicatoria pv. perforans.PLoS pathogens · 2025Article
- Genomic analyses reveal high diversity and rapid evolution ofAntimicrobial agents and chemotherapy · 2025Article
- Analysis of Piscine orthoreovirus genotype 1 genomes collected over a 32-year period (1988-2020) suggests a fitness peak in salmon hosts with minimal evidence for temporal divergence.Virus evolution · 2025Article
- Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal.PLoS computational biology · 2024Article
- Clockor2: Inferring Global and Local Strict Molecular Clocks Using Root-to-Tip Regression.Systematic biology · 2024Article
- Archival mitogenomes identify invasion by theProceedings. Biological sciences · 2024Article
- Emergence and spread ofMicrobiology spectrum · 2024Article
- Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history.Nature communications · 2023Article
- Genetic diversity and epidemic histories of rice yellow mottle virus in Ghana.Virus research · 2023Article
- Dynamics of the rice yellow mottle disease in western Burkina Faso: Epidemic monitoring, spatio-temporal variation of viral diversity, and pathogenicity in a disease hotspot.Virus evolution · 2023Article
- Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia.Science advances · 2022Article
- The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China.Virus evolution · 2022Article
- Rivers and landscape ecology of a plant virus, Rice yellow mottle virus along the Niger Valley.Virus evolution · 2021Article
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Authors and funding
5 authors.
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Abstract
Motivation: Molecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. Importantly, such inferences should only be performed on datasets displaying sufficient temporal signal, a feature important to test prior to any tip-dating inference. For this purpose, the most popular method considered to-date has been the 'root-to-tip regression' which consist in fitting a linear regression of the number of substitutions accumulated from the root to the tips of a phylogenetic tree as a function of sampling times. The main limitation of the regression method, in its current implementation, relies in the fact that the temporal signal can only be tested at the whole-tree scale (i.e. its root). Results: To overcome this limitation we introduce Phylostems, a new graphical user-friendly tool developed to investigate temporal signal within every clade of a phylogenetic tree. We provide a 'how to' guide by running Phylostems on an empirical dataset and supply guidance for results interpretation. Availability and implementation: Phylostems is freely available at https://pvbmt-apps.cirad.fr/apps/phylostems.
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