NAME

       SweeD - Assess SNPs for their contribution to genetic drift

DESCRIPTION

              SweeD version 3.1 released by Nikolaos Alachiotis and Pavlos Pavlidis in January 2013.

              SweeD | SweeD-P | SweeD-C | SweeD-P-C

       -name runName

       -input inputFile

       -grid gridNumber

              [-folded]  [-monomorphic]  [-strictPolymorphic] [-isfs inputSFS] [-osfs outputSFS] [-osf outputSF]
              [-threads  threadNumber]  [-checkpoint  checkpointInterval]  [-eN  timeT  sizeX]  [-G  rateG]  [-s
              sequences] [-h|-help] [-v|version]

       -name <STRING>
              Specifies a name for the run and the output files.

       -input <STRING>
              Specifies the name of the input alignment file.  Supported file formats: SF (Sweep Finder) format.

       -grid <INTEGER>
              Specifies the number of positions in the alignment where the CLR will be computed.

       -folded
              Considers the SFS folded (the ancestral and derived states can not be distinguished).

       -monomorphic
              Includes the monomorphic sites in the analysis. The default action is to discard them.

       -strictPolymorphic
              Does  not  include  *potential  monomorphic* sites in the analysis. These are sites where for some
              sequences the state is missing and the remaining are monomorphic.

       -isfs <STRING>
              Specifies the name of the input SFS file.

       -osfs <STRING>
              Specifies the name of the output SFS file.

       -osf <STRING>
              Specifies the name of the output SF file.

       -threads <INTEGER>
              Specifies the number of threads.

       -checkpoint <INTEGER>
              Specifies the checkpoint interval in seconds (default: 3600).

       -eN <FLOAT> <FLOAT>
              Sets population size to sizeX*N0 at time timeT, where N0 is the present-day population size.

       -G <FLOAT>
              Sets the growth rate of the population size at time 0. The growth rate continues to be exponential
              until the -eN command specifies a constant population size.

       -s <INTEGER>
              Specifies the number of sequences when no input file is provided.

       -h|-help
              Displays this help message.

SweeD                                               July 2018                                           SWEED(1)