Metadata-Version: 2.1
Name: asymmetree
Version: 0.0.1
Summary: Simulation of species and gene tree scenarios with asymmetric evolution rates.
Home-page: https://github.com/david-schaller/asymmetree
Author: David Schaller
Author-email: david@0x002A.com
License: UNKNOWN
Description: # 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](https://networkx.github.io/)
        * [Scipy and Numpy](http://www.scipy.org/install.html)
        * [Matplotlib](https://matplotlib.org/)
        
        Furthermore, to use functions involving sequence simulation and alignment, the following packages must be installed:
        * [Biopython](http://biopython.org/wiki/Download)
        * [Pyvolve](https://github.com/sjspielman/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](https://birc.au.dk/software/rapidnj/)
        * [qinfer](https://github.com/david-schaller/qinfer)
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
