See the IntelliJ-setup folder for screenshots on IntelliJ module dependencies.
The following Beast2 packages are required as dependencies:
Use ant to build packages in the following order: beast2, bdsky and beastLabs.
Then use ant package to build BeastFX, and ant to build the remaining dependencies (sampledancestors and stratigraphic-ranges).
ssRanges is a BEAST2.7 package for performing phylodynamic inference under the skyline birth-death stratigraphic ranges model. Depending on data interpretation it can be used for both macroevolution and epidemiology.
It builds on the sRanges package for the constant rate birth-death stratigraphic ranges model to support piecewise constant diversification rates
The dependencies on other BEAST2.7 packages can be found in version.xml file.
ssRanges uses three types of data to inform the inference:
- Genetic sequence alignment
- Morphological characters alignment
- Sampling data, including range of a taxa
Sampling at present and through time is allowed, as well as having sampled ancestors. The data includes the time and uncertainty of these samples. Stratigraphic ranges are represented by two nodes marking the beginning and end of taxa (species or host), and data and time uncertainty can be associated with either of these nodes. Samples of the same taxa in between are integrated out by the model and are not needed.
ssRanges produces a posterior distribution of model parameters and oriented trees:
- In the macroevolution case, they are interpreted as a budding speciation model, where each child of a node is either an ancestor or descendant species.
- In epidemiology, they are transmission trees where each child of a node is either a donor or recipient.
The TreeAnnotator tool from the sRanges package can be used to produce MCC trees. For more information, see the sRanges documentation.
You can install the latest release by adding the link https://raw.githubusercontent.com/bioDS/skyline-stratigraphic-ranges/main/package.xml as a third party BEAST package repository in Beauti and installing the ssRanges package that appears.
The Beauti template is currently not available. You can find examples of BEAST2 XML in the examples folder.
We model a labeled oriented tree on stratigraphic ranges. It contains metadata on the orientation of internal nodes, where the left child represents the ancestral species (donor), and the right child represents the descendant species (recipient). For every branch, it's metadata is recorded at the child node and represents the ancestral/descendant assignment. Sampled ancestors are always attached from the left, and appropriate metadata is recorded.
Note that while trees are logged with correct node orientation, metadata should be referenced when allocating branch label.
Clock and substitution models implemented in BEAST2 are allowed.
Pull requests are welcome. If you have major suggestions, please discuss them before any real effort is put into development.
The skyline extension to the constant rate model are developed by Kate Truman and Alexandra (Sasha) Gavryushkina. The sRanges package this relies on is developed by Alexandra (Sasha) Gavryushkina and Ugne Stolz.