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TEASPOON is a package for the inference of adaptive molecular evolution in serially-sampled population-genetic datasets.
If you use this software, please cite us - this helps us maintain and improve TEASPOON.
Overview
TEASPOON is designed to infer the counts of silent and replacement amino acid mutations in one or more population-genetic datasets, by reference to an ancestral ('outgroup') population.
This method has developed from the McDonald-Kreitman (MK) test after several years of work by Bhatt et al. (2010; 2011) and Raghwani et al. (2016; 2018 in prep.). Note that this method is intended to be used with aligned coding sequences and reasonably large datasets (it is fairly fast) but is not considered valid for inter-species data, or alignments with fewer than 30 (ideally, 100 or more) sequences.
Quick-start guide
In a hurry? See the quickstart guide.
Installation
See the installation pages for more information.
Manual
Usage information can be found here:
See here for detailed manual.
FAQs
We're compiling a frequently-asked-questions page. Bear with us as it isn't very complete!
Contact / credits
TEASPOON is written and maintained by Jayna Raghwani, Joe Parker and Oli Pybus (incorporating code from Samir Bhatt and several third-party Java libraries).
For more contact information, including bug reports and help, please see the contact pages
Licence
TEASPOON is freely available and free for academic and educational use. For commercial use please contact us
Roadmap
TEASPOON is currently versioned at 0.1.4. Following publication of the associated Application Note we'll evaluate user feedback for a year and up-version to 0.2 or 0.3 if needed.
There is no current plan to carry out major additional work on this package.