What's new in Genie 3.0
Oct 15, 2010
- Trees with non-contemporaneous tips (TipDate trees) can be read in and analysed. This should prove very useful for viral sequence data sets. Parametric demographic models and the classic skyline plot are available for TipDate trees.
- The user interface has been changed from a menu system to a command-line system. Commands can either be typed in or read from a NEXUS format file. The interface is thus similar to the command-line version of PAUP*.
- GENIE now reads and writes NEXUS format trees. PHYLIP format trees are no longer supported.
- Two new methods for optimising the generalised skyline plot have been added.
- The results can be rescaled into a real time scale using the substitution rate of the sequences concerned.
- Two new demographic models have been added; piecewise logistic growth and piecewise expansion growth.
- Lineage-through-time plots can now be outputted.
- The Kolmorgorov-Smirnov test has been removed as it is not valid for most data sets.