Divergence Time Estimation

Divergence Time Estimation

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CD Genomics provides divergence time estimation services to reveal the temporal dynamics of species formation events, understand the rate of evolutionary change, and gain insight into the origins of biodiversity. We offer comprehensive and tailored solutions to help you analyze the evolutionary patterns and rhythms throughout the tree of life.

Overview of Divergence Time Estimation

Divergence time estimation plays a crucial role in reconstructing the evolutionary history of species and can help researchers understand many aspects of biological evolution, such as feature evolution, diversification, and biogeography. With the development of next-generation sequencing technologies and bioinformatics analysis methods, as well as fossil knowledge for calibration, it is possible to obtain reliable molecular dating results. Many methods exist for converting branch lengths to be proportional to time. However many of these methods do not scale well to the phylogeny of thousands of taxa. As the size of phylogenies increases, there is a need to explore the best methods for divergence time estimation using large amounts of data. One potential solution is to focus attention on a subset of the data for divergence time estimation, which can significantly reduce the computational burden and avoid the problem of data heterogeneity that can lead to biased results.

Fig. 1. Divergence time estimation between speciesFig. 1. Divergence time estimation between species. (Vialle R A, et al, 2018)

Application Field

With a state-of-the-art bioinformatics pipeline, CD Genomics can process and analyze large-scale genomic datasets to accurately estimate divergence times. By combining powerful computational algorithms, statistical models, and machine learning techniques, CD Genomics is able to accurately and efficiently cope with the complexity of divergence time estimation. We offer a comprehensive set of services to meet the diverse needs of our clients exploring evolutionary relationships and timelines.

  • Biology. By accurately estimating divergence times, we can help you elucidate the rhythms and patterns of evolutionary events, revealing key insights into the evolutionary forces that shape biodiversity.
  • Phylogenetics. By inferring divergence times, our experts can construct phylogenetic trees that describe branching patterns and relationships among different species. These trees serve as a framework for studying evolutionary processes, classifying organisms, and predicting the emergence of new features.
  • Conservation biology. We can help you assess the historical relationships between populations and species.

Workflow of Divergence Time Estimation

CD Genomics offers a streamlined process for divergence time estimation that integrates computational methods, statistical modeling, and genomic data analysis. We will ensure accurate and reliable results for our customers.

(1) Data acquisition and pre-processing. CD Genomics uses high-throughput sequencing technology to generate extensive datasets, which are then subjected to quality control procedures to filter out artifacts and ensure data integrity.

(2) Phylogenetic inference: CD Genomics uses advanced algorithms and phylogenetic inference methods to construct robust phylogenetic trees from the acquired genomic data to capture the evolutionary history of taxa of interest.

(3) Model selection: To estimate divergence times, researchers must select an appropriate model to explain evolutionary processes such as mutation rates, substitution patterns, and population dynamics. CD Genomics assists in model selection by employing statistical methods, model testing, and validation techniques.

(4) Dispersal time estimation: CD Genomics employs sophisticated computational algorithms, including penalized likelihood methods and Bayesian methods, to estimate dispersion times from molecular data. These methods incorporate statistical uncertainty and take into account factors such as gene tree inconsistency and incomplete genealogical classification.

(5) Validation and interpretation: CD Genomics fully validates the estimated divergence times by statistical analysis, bootstrap, and cross-validation techniques.

CD Genomics provides comprehensive bioinformatics services to accurately estimate divergence times, designed to help you unlock the mysteries of evolutionary history and understand the diversity of species of origin. By combining cutting-edge technology, powerful algorithms, and expert analysis, CD Genomics enables researchers to explore the complexity of evolutionary timelines and deepen our understanding of the processes that shaped life on Earth. If you are interested in our services, please contact us for more detailed information.


  1. Vialle R A, de Souza J E S, Lopes K P, et al. Whole genome sequencing of the pirarucu (Arapaima gigas) supports independent emergence of major teleost clades[J]. Genome biology and evolution, 2018, 10(9): 2366-2379.
* For Research Use Only. Not for use in diagnostic procedures.
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