SWEED(1)

✨ SweeD: the SNP sweep detective ✨

🧬 NAME 🧬

Okay so SweeD is the tool that assesses SNPs for how much they contribute to genetic drift. It's giving science and it's giving main character energy 💅

🎀 DESCRIPTION 🎀

Okay bestie, SweeD version 3.1 dropped in January 2013, made by Nikolaos Alachiotis and Pavlos Pavlidis 💖 There are four flavors of it: SweeD | SweeD-P | SweeD-C | SweeD-P-C ✨

Here's the basic vibe for how you call it:

-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]

Now let's go through the options one by one, no cap 🦋

• -name <STRING> — Give your run a name 🌸 It's used for the run and the output files, so pick something you'll recognize later.
• -input <STRING> — The name of your input alignment file 📂 The format it's looking for is SF (Sweep Finder) format.
• -grid <INTEGER> — How many positions in the alignment get a CLR computed 🔥
• -folded — Treats the SFS as folded, which means the ancestral and derived states can't be told apart 🙈
• -monomorphic — Includes the monomorphic sites in the analysis ✨ Default move is to discard them, so you have to ask for this one specifically.
• -strictPolymorphic — Leaves out potential monomorphic sites 💜 Those are the sites where some sequences have a missing state and the rest are monomorphic.
• -isfs <STRING> — The name of your input SFS file 🎀
• -osfs <STRING> — The name of your output SFS file 🌈
• -osf <STRING> — The name of your output SF file 🦋
• -threads <INTEGER> — How many threads you want 🧚
• -checkpoint <INTEGER> — The checkpoint interval in seconds (default: 3600) ⭐
• -eN <FLOAT> <FLOAT> — Sets the 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 stays exponential until -eN specifies a constant population size, so keep that in mind.
• -s <INTEGER> — The number of sequences, for when you don't have an input file 🍓
• -h|-help — Displays the help message 🫶

Bestie, that's the whole tea ☕ SweeD, July 2018, and I'm out. Ttyl, stay iconic 💖🦋✨