polyDFE infers the distribution of fitness effects (DFE) of new mutations from polymorphism, and, if available, divergence data obtained from an outgroup. The polymorphism data is given through the unfolded site frequency spectrum (SFS). Note that, in order to obtain an unfolded SFS, at least one outgroup is needed. However, including the divergence data when inferring the DFE can lead to bias in the estimated parameters.
Once the DFE is obtained, polyDFE also calculates alpha, the rate of adaptive molecular evolution.
polyDFEv2.0 can fit jointly multiple datasets for which some parameters can be set to be invariant (shared across the datasets). This enables model testing for parameter invariance, for example, testing if different datasets have the same DFE or not.
More details can be found in
If using this software in a publication, please cite the above articles.
Paula Tataru, paula.tataru at gmail . com
polyDFE can be ran using the provided pre-compiled binaries for Windows, Linux and iOS.
polyDFE is implemented in C and uses the GSL library. For compiling polyDFE, the GSL library should be downloaded from https://www.gnu.org/software/gsl/ and compiled accordingly. polyDFE has been tested using GSL-1.16. Note that polyDFE does not work with a newer version of GSL.
The simplest way to compile polyDFE:
cd to the directory containing the makefile and type
make all to compile the code.
You can remove the program binaries and object files from the
source code directory by typing make clean.
If the GSL library is not installed in the default directory, than the installation path needs to be specified in the makefile by updating USR_INC and USR_LIB and uncommenting the lines at the top of the makefile.
polyDFEv2.0 is also distributed as pre-compiled binaries for Windows, Linux and macOS.
For more details on running polyDFE, please consult the manual and tutorial.
See the file LICENSE.txt for information on terms & conditions for usage, and a DISCLAIMER OF ALL WARRANTIES.