ArticleBMC evolutionary biology2014
Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data.
Article in BMC evolutionary biology, 2014. 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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15 citing papers in PubMed.
- torchtree: Flexible Phylogenetic Model Development and Inference Using PyTorch.Systematic biology · 2026Article
- Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model.Systematic biology · 2024Article
- Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock.Genome biology and evolution · 2024Review
- Automatic Differentiation is no Panacea for Phylogenetic Gradient Computation.Genome biology and evolution · 2023Article
- 19 Dubious Ways to Compute the Marginal Likelihood of a Phylogenetic Tree Topology.Systematic biology · 2020Article
- A new method for inferring timetrees from temporally sampled molecular sequences.PLoS computational biology · 2020Article
- Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics.PeerJ · 2019Article
- Genome-scale analysis of evolutionary rate and selection in a fast-expanding Spanish cluster of HIV-1 subtype F1.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2018Article
- Article
- The impact of migratory flyways on the spread of avian influenza virus in North America.BMC evolutionary biology · 2017Article
- Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks.Molecular biology and evolution · 2017Article
- Inferences from tip-calibrated phylogenies: a review and a practical guide.Molecular ecology · 2016Review
- Seqotron: a user-friendly sequence editor for Mac OS X.BMC research notes · 2016Article
- Bayesian molecular clock dating of species divergences in the genomics era.Nature reviews. Genetics · 2016Review
- Avian influenza virus exhibits distinct evolutionary dynamics in wild birds and poultry.BMC evolutionary biology · 2015Article
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Abstract
backgroundEarly methods for estimating divergence times from gene sequence data relied on the assumption of a molecular clock. More sophisticated methods were created to model rate variation and used auto-correlation of rates, local clocks, or the so called "uncorrelated relaxed clock" where substitution rates are assumed to be drawn from a parametric distribution. In the case of Bayesian inference methods the impact of the prior on branching times is not clearly understood, and if the amount of data is limited the posterior could be strongly influenced by the prior.
resultsWe develop a maximum likelihood method--Physher--that uses local or discrete clocks to estimate evolutionary rates and divergence times from heterochronous sequence data. Using two empirical data sets we show that our discrete clock estimates are similar to those obtained by other methods, and that Physher outperformed some methods in the estimation of the root age of an influenza virus data set. A simulation analysis suggests that Physher can outperform a Bayesian method when the real topology contains two long branches below the root node, even when evolution is strongly clock-like.
conclusionsThese results suggest it is advisable to use a variety of methods to estimate evolutionary rates and divergence times from heterochronous sequence data. Physher and the associated data sets used here are available online at http://code.google.com/p/physher/.
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