# Sweepfinder2


{{< admonition success "Installed" true >}}
This software should be available with no extra configuration.
{{< /admonition >}}

## sweepfinder2

A program written in C that can perform genomic scans for recent selective
sweeps selection while controlling for background selection and mutation rate
variation.

Please cite the following manuscript if using this software:
M DeGiorgio, CD Huber, MH Hubisz, I Hellmann, R Nielsen (2016) SweepFinder2:
increased sensitivity, robustness, and flexibility. Bioinformatics
32:1895-1897.

### Link to manual

[Link to the pdf manual](../docs/sweepfinder2/Manual_SweepFinder2_v1.0.pdf)

-------------------------------------------------------------------------------

## Location

```console
$ which SweepFinder2
/local/cluster/bin/SweepFinder2
```

## help message

```console
$ SweepFinder2 --help
usage:
	to get frequency spectrum: ./SweepFinder2 -f CombinedFreqFile SpectFile
	to find sweeps:
		./SweepFinder2 -s G FreqFile OutFile
		./SweepFinder2 -sg g FreqFile OutFile
		./SweepFinder2 -su GridFile FreqFile OutFile
	to find sweeps using a pre-computed frequency spectrum:
		./SweepFinder2 -l G FreqFile SpectFile OutFile
		./SweepFinder2 -lg g FreqFile SpectFile OutFile
		./SweepFinder2 -lu GridFile FreqFile SpectFile OutFile
	to find sweeps using pre-computed frequency spectra given recombination map:
		./SweepFinder2 -lr G FreqFile SpectFile RecFile OutFile
		./SweepFinder2 -lrg g FreqFile SpectFile RecFile OutFile
		./SweepFinder2 -lru GridFile FreqFile SpectFile RecFile OutFile
	to find sweeps using pre-computed frequency spectra given B values:
		./SweepFinder2 -lb G FreqFile SpectFile BValFile N1 N2 T OutFile
		./SweepFinder2 -lbg g FreqFile SpectFile BValFile N1 N2 T OutFile
		./SweepFinder2 -lbu GridFile FreqFile SpectFile BValFile N1 N2 T OutFile
	to find sweeps using pre-computed frequency spectra given recombination map and B values:
		./SweepFinder2 -lrb G FreqFile SpectFile RecFile BValFile N1 N2 T OutFile
		./SweepFinder2 -lrbg g FreqFile SpectFile RecFile BValFile N1 N2 T OutFile
		./SweepFinder2 -lrbu GridFile FreqFile SpectFile RecFile BValFile N1 N2 T OutFile
```

software ref: <http://degiorgiogroup.fau.edu/sf2.html>  
research ref: <https://doi.org/10.1093/bioinformatics/btw051>