Mutations that accumulate in the genome of replicating biological organisms can be used to infer their evolutionary history. In case of measurably evolving organisms genomes often reveal their detailed spatio-temporal spread. Such phylodynamic analyses are particularly useful to understand the epidemiology of rapidly evolving viral pathogens. The volume of genome sequences available for different pathogens, however, have increased dramatically over the last couple of years and traditional methods for phylodynamic analysis scale poorly with growing data sets. 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 run time of TreeTime scales linearly with data set size.
- Downloaded 1,460 times
- Download rankings, all-time:
- Site-wide: 13,548
- In evolutionary biology: 454
- Year to date:
- Site-wide: 62,313
- Since beginning of last month:
- Site-wide: 87,061
Downloads over time
Distribution of downloads per paper, site-wide
- 27 Nov 2020: The website and API now include results pulled from medRxiv as well as bioRxiv.
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!