.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH SWEED "1" "July 2018" "SweeD " "User Commands"
.SH NAME
SweeD \- Assess SNPs for their contribution to genetic drift
.SH DESCRIPTION
.IP
SweeD version 3.1 released by Nikolaos Alachiotis and Pavlos Pavlidis in January 2013.
.IP
SweeD | SweeD\-P | SweeD\-C | SweeD\-P\-C
.HP
\fB\-name\fR runName
.HP
\fB\-input\fR inputFile
.HP
\fB\-grid\fR gridNumber
.IP
[\-folded]
[\-monomorphic]
[\-strictPolymorphic]
[\-isfs inputSFS]
[\-osfs outputSFS]
[\-osf outputSF]
[\-threads threadNumber]
[\-checkpoint checkpointInterval]
[\-eN timeT sizeX]
[\-G rateG]
[\-s sequences]
[\-h|\-help]
[\-v|version]
.TP
\fB\-name\fR <STRING>
Specifies a name for the run and the output files.
.TP
\fB\-input\fR <STRING>
Specifies the name of the input alignment file.
Supported file formats: SF (Sweep Finder) format.
.TP
\fB\-grid\fR <INTEGER>
Specifies the number of positions in the alignment where the CLR will be computed.
.TP
\fB\-folded\fR
Considers the SFS folded (the ancestral and derived states can not be distinguished).
.TP
\fB\-monomorphic\fR
Includes the monomorphic sites in the analysis. The default action is to discard them.
.TP
\fB\-strictPolymorphic\fR
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.
.TP
\fB\-isfs\fR <STRING>
Specifies the name of the input SFS file.
.TP
\fB\-osfs\fR <STRING>
Specifies the name of the output SFS file.
.TP
\fB\-osf\fR <STRING>
Specifies the name of the output SF file.
.TP
\fB\-threads\fR <INTEGER>
Specifies the number of threads.
.TP
\fB\-checkpoint\fR <INTEGER>
Specifies the checkpoint interval in seconds (default: 3600).
.TP
\fB\-eN\fR <FLOAT> <FLOAT>
Sets population size to sizeX*N0 at time timeT, where N0 is the present\-day population size.
.TP
\fB\-G\fR <FLOAT>
Sets the growth rate of the population size at time 0. The growth rate continues to be exponential until
the \fB\-eN\fR command specifies a constant population size.
.TP
\fB\-s\fR <INTEGER>
Specifies the number of sequences when no input file is provided.
.TP
\fB\-h\fR|\-help
Displays this help message.