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.