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

• Python 2.7 or higher
• DendroPy Phylogenetic Computing Library, Version 4 or above
• R
• The following R packages:
  • adegenet
  • picante
  • BioGeoBears
  • GEIGER

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.