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.
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
.
If you later want to update TruSD, use the pip command:
pip3 install --upgrade trusd
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).
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.