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archipelago
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examples
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LICENSE.rst
MANIFEST.in
README.md
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archipelago.pdf
clean.sh
setup.py

README.md

Archipelago

Introduction

This is a suite of programs to generate and analyze data under the Archipelago model. It consists of four programs:

  • archipelago-profile-trees.py Calculates summary statistics for trees. Typically, this is used to derive the calibration process parameter values for the simulator.

  • archipelago-simulate.py Simulates data under the "Archipelago" model. Typically, this is used to generate phylogenies to be used to derive the training data sets.

  • archipelago-summarize.py Calculates 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.py Given a set of training data (summary statistics) and target data, classifies the target data using a Discriminant Analysis of Principal Components (DAPC).

Installation

Pre-requisites

Installing from Source

Run the following in the top-level directory of the project:

$ python setup.py install

Documentation

Full documentation is available online here:

http://jeetsukumaran.github.io/archipelago

or in the archipelago.pdf document found in the root directory of the project.