TruSD

Trajectories under Selection and Drift is an implementation of a method that co-infers selection coefficients and genetic drift from allele trajectories using a maximum-likelihood framework.

If you find the software useful in your research please cite this package.

Installation

TruSD needs Python 3.6 or newer. Python 2 is not supported! TruSD was only tested on Linux (Ubuntu), but should work on Mac and Windows as well.

We suggest to use a virtual environment for use of TruSD. To install TruSD, run:

pip3 install trusd  # add --user to install only for the user

This will install TruSD as importable module and three command line tools, trusd, trusd-plot, and trusd-sim.

Update

If you later want to update TruSD, use the pip command:

pip3 install --upgrade trusd

Running TruSD from within a Python script

Import the trusd module from your Python 3 script:

# inside python3 script or interactive prompt
import trusd
help(trusd.trusd) # gives package content

For an example, download two files (for example with wget):

wget https://github.com/mathiasbockwoldt/TruSD/blob/master/examples/min_working_example.py
wget https://github.com/mathiasbockwoldt/TruSD/blob/master/examples/traj_example.txt

You can start an example run with

python3 min_working_example.py

The min_working_example.py is documented to explain the basic steps. It uses traj_example.txt as input and produces outfile.txt (the results), outfile.json (the metadata) and outfile.pdf (the plot).

Running TruSD as command line program

The command line programs are self-explanatory using the --help flag.

trusd --help
trusd-plot --help
trusd-sim --help

The parameters are the same as in the Python modules.