---
name: "SweeD"
section: "1"
platform: "linux"
package: "sweed"
version: "3.2.1+dfsg-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/SweeD"
---

# SweeD(1)

Assess SNPs for their contribution to genetic drift

## 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.