The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
TreeTime: Maximum-likelihood phylodynamic analysis
Open accessAbstract
Mutations that accumulate in the genome of cells or viruses can be used to infer their evolutionary history. In the case of rapidly evolving organisms, genomes can reveal their detailed spatiotemporal spread. Such phylodynamic analyses are particularly useful to understand the epidemiology of rapidly evolving viral pathogens. As the number of genome sequences available for different pathogens has increased dramatically over the last years, phylodynamic analysis with traditional methods becomes challenging as these methods scale poorly with growing datasets. Here, we present TreeTime, a Python-based framework for phylodynamic analysis using an approximate Maximum Likelihood approach. TreeTime can estimate ancestral states, infer evolution models, reroot trees to maximize temporal signals, estimate molecular clock phylogenies and population size histories. The runtime of TreeTime scales linearly with dataset size.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
Relaxed Phylogenetics and Dating with Confidence
Drummond, A. J., Ho, S. Y. W., Phillips, M. J., & Rambaut, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040088 · Cited by 6,463 · cited 2×
“Models that allow for clock-rate variation have been proposed (Drummond et al. , 2006; Hasegawa et al. , 1989; Yoder and Yang, 2000).”
BackgroundEvolutionary divergence and convergence in proteins.
ZUCKERKANDL, E., & PAULING, L. (1965) · Evolving Genes and Proteins · doi:10.1016/b978-1-4832-2734-4.50017-6 · Cited by 3,020
Sanderson, M. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.301 · Cited by 1,906
Estimating the rate of evolution of the rate of molecular evolution
Thorne, J. L., Kishino, H., & Painter, I. S. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025892 · Cited by 1,317 · cited 1×
“These models typically regularize the clock-rate through a prior and penalize rapid changes of the rate by coupling the rate along branches – known as autocorrelated or local molecular clock (Aris-Brosou et al. , 2002; Thorne et al. , 1998).”
BackgroundEstimation of primate speciation dates using local molecular clocks.
Yoder, A. D., & Yang, Z. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026389 · Cited by 494
Rambaut, A. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.4.395 · Cited by 418
Aris-Brosou, S., & Yang, Z. (2002) · Systematic Biology · doi:10.1080/10635150290102375 · Cited by 230 · cited 1×
“These models typically regularize the clock-rate through a prior and penalize rapid changes of the rate by coupling the rate along branches – known as autocorrelated or local molecular clock (Aris-Brosou et al. , 2002; Thorne et al. , 1998).”
Background
Cited by
Nextstrain: real-time tracking of pathogen evolution
Hadfield, J., Megill, C., Bell, S. M., Huddleston, J., Potter, B., Callender, C., Sagulenko, P., Bedford, T., & Neher, R. A. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty407 · Cited by 3,154
Self-citationSpread of a SARS-CoV-2 variant through Europe in the summer of 2020
Hodcroft, E. B., Zuber, M., Nadeau, S., Vaughan, T. G., Crawford, K. H. D., Althaus, C. L., Reichmuth, M. L., Bowen, J. E., Walls, A. C., Corti, D., et al. (2021) · Nature · doi:10.1038/s41586-021-03677-y · Cited by 425
Self-citationSixteen novel lineages of SARS-CoV-2 in South Africa
Tegally, H., Wilkinson, E., Lessells, R. J., Giandhari, J., Pillay, S., Msomi, N., Mlisana, K., Bhiman, J. N., von Gottberg, A., Walaza, S., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01255-3 · Cited by 349
Off-season RSV epidemics in Australia after easing of COVID-19 restrictions
Eden, J.-S., Sikazwe, C., Xie, R., Deng, Y.-M., Sullivan, S. G., Michie, A., Levy, A., Cutmore, E., Blyth, C. C., Britton, P. N., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30485-3 · Cited by 340
Rockett, R. J., Arnott, A., Lam, C., Sadsad, R., Timms, V., Gray, K.-A., Eden, J.-S., Chang, S., Gall, M., Draper, J., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-1000-7 · Cited by 325
Metadata
- Authors
- Sagulenko, P., Puller, V., & Neher, R. A.
- Venue
- Virus Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-01-01
- Volume
- 4
- Issue
- 1
- Pages
- vex042-vex042
- ISSN
- 2057-1577 (ISSN-L)
- OpenAlex
- W2951878836
- Cited by
- 1,186
- References
- 8
- FWCI
- 13.39
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: TreeTime: Maximum-likelihood phylodynamic analysis. https://app.cochat.ai/papers/10.1093/ve/vex042
- The paper
- Sagulenko, P., Puller, V., & Neher, R. A. (2018). TreeTime: Maximum-likelihood phylodynamic analysis. Virus Evolution. https://doi.org/10.1093/ve/vex042
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
