TempEst

TempEst is a tool for investigating the temporal signal and 'clocklikeness' of molecular phylogenies. It can read and analyse contemporaneous trees (where all sequences have been collected at the same time) and dated-tip trees (where sequences have been collected at different dates). It is designed for analysing trees that have not been inferred under a molecular-clock assumption to see how valid this assumption may be. It can also root the tree at the position that is likely to be the most compatible with the assumption of the molecular clock.

Citation:
Rambaut, Lam, de Carvalho & Pybus (2016) Exploring the temporal structure of heterochronous sequences using TempEst. Virus Evolution 2: vew007 DOI: http://dx.doi.org/10.1093/ve/vew007

This package was formerly known as 'Path-O-Gen'.

Version History

2019-06-13 - v1.5.3
Packaging updates
New features:
  • Updating packaging for Mac and Windows versions
2017-08-30 - v1.5.1
Packaging updates
New features:
  • Updating packaging for Mac and Windows versions
2016-04-01 - v1.5
Renamed TempEst.
New features:
  • New name, TempEst (formerly Path-O-Gen)
  • Re-organization of user-interface
2013-04-23 - v1.4
Improved date parsing
New features:
  • Improved the date parsing. Will now read dates with variable precision.
  • Can specify date precision in table. These are shown as bars in the plot
  • Minor other tweaks
2010-11-03 - v1.3
Improved root finding and an MRCA trace feature
New features:
  • Improved the root optimization to use linear regression - should be more robust
  • Can import Newick as well as NEXUS tree files
  • A new feature: MRCA trace which shows a trace from selected tips to the interpolated position of their MRCA. This can help find anomalous tips (perhaps indicating contamination or mislabelling).
2009-11-27 - v1.2
More plots and linked selection of taxa
New features:
  • Added the ability to select points in the plots and the equivalent taxa will be highlighted in the tree (and vice-versa).
  • Added a residual plot for time-sampled trees. This shows the distribution of residual from the regression line to look for outliers.
2009-02-23 - v1.1
Improvements to the tree viewer
New features:
  • Added a more flexible tree viewing component (based on FigTree)
  • Tips of a dated tip tree are now shown coloured by their residual from the root to tip regression line (blue: above, red: below, black on the regression).
2009-02-12 - v1.0
First released version.
 
Andrew Rambaut, 2007