An intuitive total-evidence method for combining sequence and structural information in a phylogenetic analysis. This package is still in pre-release and has not yet been published.
BEAST 2 implementation of a stochastic Dollo model where sequence elements are acquired with an acquisition rate, and then mutate down a tree under standard substitution models. The elements can be irreversibly deleted with a loss rate. This model is suitable for biological and linguistic data, and was adapated from the stochastic Dollo model by Nicholls and Gray 2008.
This package requires BEAST 2.7 or newer
- Launch BEAUti
- Click on File -> Manage Packages
- Install IndelDollo. If IndelDollo is not in the list of packages, you may need to add an extra package repository as follows:
- click the packager repositories button. A dialog pops up.
- click the Add URL button. A dialog is shown where you can enter https://raw.githubusercontent.com/CompEvol/CBAN/master/packages-extra-2.7.xml
- click the OK button. There should be an extra entry in the list.
- click Done
- After a short delay, IndelDollo should appear in the list of packages.
Please see the examples/ folder for working XML files. At this stage, IndelDollo analyses cannot be generated using BEAUti.
The pruned trees in any given log file may have differing taxonsets. This stumps most of the tree parsers in BEAST2. To summarise a posterior distribution of pruned trees, use the PrunedTreeAnnotator tool in IndelDollo:
path/to/beast/bin/applauncher PrunedTreeAnnotator -burnin 10 -trees in.trees -out mcc.tree
This method first finds the most commonly occurring taxonset, and then finds the maximum clade credibility (mcc) tree among the trees which share that taxonset.
Nicholls, Geoff K., and Russell D. Gray. "Dated ancestral trees from binary trait data and their application to the diversification of languages." Journal of the Royal Statistical Society: Series B (Statistical Methodology) 70.3 (2008): 545-566.