Frequently Asked Questions

Q: How did you derive the molecular time estimates?

The molecular time estimates were obtained from scientific literature.

Q: How did you derive confidence intervals and min-max ranges?

For molecular time estimates derived from >= 5 time estimates from the scientific literature, a t-distribution is used to calculate a confidence interval for the molecular time estimate. When between 2 and 4 time estimates from the scientific literature are used to calculate a molecular time estimate, a range (min and max time estimates) is provided instead of a confidence interval. When only 1 time estimate from the scientific literature is available, no range or confidence interval is provided.

Q: How do you calculate the summary times?

Summary time estimates are calculated using a simple average and a weighted average based on the number of genes analyzed. The weighted average for each data type is calculated in addition to the overall weighted average.

Q: What search method is employed to locate molecular time estimates for a pair of taxa?

When a valid pair of taxa is submitted through the search page, the TimeTree Database determines the most inclusive taxonomic groups for each query taxa. Such groups are one level lower in the taxonomic classification than the common taxon that includes both query taxa. Once these groups are determined, the TimeTree Database obtains all molecular time estimates in which a member of the most inclusive group for Taxon A is compared to a member of the most inclusive group for Taxon B.

Q: How do I cite the TimeTree database?

Hedges SB, Marin J, Suleski M, Paymer M & Kumar S (2015) Tree of Life Reveals Clock-Like Speciation and Diversification. Mol Biol Evol 32: 835-845.

Kumar S & Hedges SB (2011) TimeTree2: species divergence times on the iPhone. Bioinformatics 27:2023-2024.

Hedges SB, Dudley J, & Kumar S (2006). TimeTree: A public knowledge-base of divergence times among organisms. Bioinformatics 22: 2971-2972.

Q: Can I download the TimeTree Database data on to my computer?

The TimeTree Database data is currently not available for download. Methods for making these data available in the future are currently under discussion.

Q: I found an error on the TimeTree website. How can I report it?

Errors and suggestions can be submitted using the contact page.

Q: Can I get a list of the literature referenced by the TimeTree Database?

Yes, please click here to view a complete list of references.

Q: How often is the TimeTree Database updated?

Currently, the TimeTree Database is updated periodically, because each update requires changes to the large guide tree. In the future, updates will occur more frequently or continuously as new literature appears.

Q: Can I submit my own, unpublished, molecular time estimate to the TimeTree Database?

The TimeTree Database currently relies solely on published data and is not presently accepting unpublished time estimates.

Q: What software was used to create the TimeTree Database and Website?

The TimeTree Database was developed using the PostgreSQL database server. The web interface was developed with PHP.

Q: Why are the calibrations not listed for each study?

Calibrations are important in timing but they are used in different ways by different investigators. For example they can be used as minimums, maximums, fixed points, and with different distributions (e.g., lognormal, exponential, uniform). Two studies with identical calibrations could present greatly different time estimates because of this complexity in methodology. If you have questions about such details, it is advisable to refer to the original studies.

Q: Why is the time estimation method not listed for each study?

There are many methods of time estimation and many options that can be used with each method. Two studies with identical data, calibrations, and using the same software, can yield different time estimates depending on how the software was used. If you have questions about such details, it is advisable to refer to the original studies.