asymmetree 0.0.1

Simulation of species and gene tree scenarios with asymmetric evolution rates.

Gene Tree Simulator and Best Match Inference

Overview

Simulator for species and gene trees

Framework for the realistic simulation of species and gene tree scenarios with asymmetric evolution rates. The following steps are implemented in the Python package asymmetree.simulator:

• species tree simulation ('innovation model')
• gene tree simulation (Gillespie algorithm)
• gene tree imbalancing (asymmetric evolution rates of paralogous genes)
• computation of a (noisy) distance matrix from the gene tree

Best Match Inference

Inference of the best match relation either directly from the gene tree or from a distance matrix (several methods).

• asymmetree.best_matches

Dependencies

AssymmeTree has several dependencies:

• NetworkX
• Scipy and Numpy
• Matplotlib

Furthermore, to use functions involving sequence simulation and alignment, the following packages must be installed:

• Biopython
• Pyvolve

To use the tree reconstruction method for best match inference and the C++ implementation of the quartet method, resp., the following software must be installed (I recommend that you compile these tools on your machine, place the binaries into a persistent location and add this location to your PATH environment variable):

• RapidNJ
• qinfer