Installed
This software should be available with no extra configuration.
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
Location
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$ which SweepFinder2
/local/cluster/bin/SweepFinder2
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help message
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$ 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
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software ref: http://degiorgiogroup.fau.edu/sf2.html
research ref: https://doi.org/10.1093/bioinformatics/btw051