SweeD - Assess SNPs for their contribution to genetic drift
- 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.