EcoPhylo

Ecophylo is dedicated to coalescent-based simulation of eco-evolutionary dynamics. Species assemblages and their shared ancestry can be simulated by jointly taking into account the influence of past demographic fluctuations and extinctions along with how divergent genotypes have introduced new species over time through speciation.

The source for this project is available here.

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Dependencies

This package depend on python 3.7.

There are multiple dependencies to other python packages. This will be done when installing ecophylo tool in most cases.

You can experiment difficulties for installing msprime, check the help here

Install (with pip)

To install this package, you can either download the tar.gz file in the dist directory of the repository :

python3 -m pip install <path_to>/ecophylo-<VERSION>.tar.gz

or install from the Python Package index (Pypi) :

python3 -m pip install ecophylo

or install from github (it does not work for private repository):

python3 -m pip install git+https://github.com/thegreatlizzyator/ecophylo/tree/packaging/dist/ecophylo-0.0.5.tar.gz

Usage

You can simulate trees using this package main function in python.

import ecophylo
n = 25 #the number of sampled individuals
com_size = [[5000,10000,50000]] # the size of the assemblage in the past, the first element is the current assemblage size
mu = 0.001 # the point mutation rate
changetime = [[0,700,10000]] # the dates (in generation time) at which the assemblage has changed sizes in the past

tree = ecophylo.simulate(samples = n,
                         com_size= com_size, 
                         mu = mu, 
                         changetime= changetime, seed= 42)

print(tree)

Maintainers

@thegreatlizzyator & @gowachin.

Contributing

Feel free to dive in! Open an issue or submit PRs.

thegreatlizzyator follows the Contributor Covenant Code of Conduct.

Contributors

This project exists thanks to all the people who contribute.

License

CeCILL-B © Elizabeth Bathelemy