This is a suite of programs to generate and analyze data under the Archipelago model. It consists of four programs:
archipelago-profile-trees.pyCalculates summary statistics for trees. Typically, this is used to derive the calibration process parameter values for the simulator.
archipelago-simulate.pySimulates data under the "Archipelago" model. Typically, this is used to generate phylogenies to be used to derive the training data sets.
archipelago-summarize.pyCalculates summary statistics for one or more phylogenies. This will be used to derive the target data from an empirical phylogeny as well as the training data from simulated phylogenies.
archipelago-classify.pyGiven a set of training data (summary statistics) and target data, classifies the target data using a Discriminant Analysis of Principal Components (DAPC).
- Python 2.7 or higher
- DendroPy Phylogenetic Computing Library, Version 4 or above
- The following R packages:
Installing from Source
Run the following in the top-level directory of the project:
$ python setup.py install
Full documentation is available online here:
or in the
archipelago.pdf document found in the root directory of the