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.