Import Debian changes 3.2.1+dfsg-1

The unfortunate original tarball contained object files.

.\" 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.

sweed (3.2.1+dfsg-1) unstable; urgency=medium

  * Initial release (Closes: #902960)

 -- Steffen Moeller <moeller@debian.org>  Wed, 04 Jul 2018 00:25:27 +0200

11

Source: sweed

Section: science

Priority: optional

Maintainer: Steffen Moeller <moeller@debian.org>

Build-Depends: debhelper (>= 11)

Standards-Version: 4.1.3

Homepage: https://sco.h-its.org/exelixis/web/software/sweed/

Vcs-Browser: https://salsa.debian.org/med-team/sweed

Vcs-Git: https://salsa.debian.org/med-team/sweed.git

Package: sweed

Architecture: any

Depends: ${shlibs:Depends}, ${misc:Depends}

Description: assessment of SNPs for their evolutionary advantage

 Biological sequences are available in ever increasing abundance across

 ever larger populations for ever increasing fractions of the genome. This

 tool sorts the SNPs for their active or passive contribution to a genetic

 drift, i.e. to see particular sequences at a higher fraction over time.