PAIR_ALIGN(1)

💅 PAIR_ALIGN — bestie, let's align some sequences 💅

okay so this is pair_align, a manual page from section 1 (that's "general commands", the little number after the name, iykyk ✨). Fr fr, it's the tool for pairwise alignment and she ate.

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🌸 NAME 🌸

pair_align — Pairwise alignment. That's it, that's the name, no cap. 💖

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🦋 SYNOPSIS 🦋

pair_align [OPTIONS] -s IN

like, you give her options, you give her an input file with -s, and she goes to work. simple as. ✨

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👑 DESCRIPTION 👑

so basically this program lets you align two sequences using dyamic programming alignment algorithms — yes bestie, the manpage itself says "dyamic", we keep it exactly as-is, typos are sacred, periodt 💀 — while also letting you tweak various parameters to your little heart's content. it's giving customizable. it's giving control. 🎀

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🔥 OPTIONS 🔥

• -h, --help — shows you the help message. bestie behavior honestly, always ask for help when you need it 🫶
• --version — spills the version info. 💅

⭐ Main Options

• -s, --seq INPUT_FILE — the FASTA file with two sequences in it. the valid filetypes are: .frn, .fna, .ffn, .fasta, .fas, .faa, and .fa. pick one, don't be chaotic 🌸
• -a, --alphabet STRING — the sequence alphabet. literally one of protein, dna, rna, and text. Default: protein. 💜
• -m, --method STRING — the DP alignment method, and your choices are Needleman-Wunsch, Gotoh, Smith-Waterman, Longest Common Subsequence — or in shortcode: one of nw, gotoh, sw, and lcs. Default: gotoh. main character method honestly ✨
• -o, --outfile OUTPUT_FILE — the output filename. valid filetypes are: .msf, .frn, .fna, .ffn, .fasta, .fas, .faa, and .fa. Default: out.fasta. 🦋

🎀 Scoring Options

• -g, --gop INTEGER — gap open penalty. Default: -11. ouch, that's a big yikes number but ok 👑
• -e, --gex INTEGER — gap extension penalty. Default: -1. gentler, we love a soft penalty 💖
• -ma, --matrix STRING — the score matrix. yes queen, matrix 🧚
• -ms, --msc INTEGER — match score. Default: 5. slay, a match! ⭐
• -mm, --mmsc INTEGER — mismatch penalty. Default: -4. not me getting penalized for being different 😭

🌈 Banded Alignment Options

• -lo, --low INTEGER — the lower diagonal. 📉
• -hi, --high INTEGER — the upper diagonal. 📈

💀 DP Matrix Configuration Options

• -c, --config STRING — the alignment configuration. one of ffff, ffft, fftf, fftt, ftff, ftft, fttf, fttt, tfff, tfft, tftf, tftt, ttff, ttft, tttf, and tttt. yes bestie, ALL sixteen combinations, we listed every single one, no skipping 🙈

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🧚 ALIGNMENT CONFIGURATION 🧚

so the alignment configuration is a string of four characters, and each one of them is either t or f. every single combination is allowed — she's flexible like that 💅. here's what they all mean, one by one:

• tfff — first row initialized with 0s. 🍓
• ftff — first column initialized with 0s. 🍓
• fftf — search last column for maximum. 🔥
• ffft — search last row for maximum. 🔥

ngl bestie, that block above is exactly what the original gives us, so that's exactly what you get. no extra lore, no invented facts, we stay honest in this house 🫶

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💖 a lil sign-off 💖

this gorgeous piece of documentation is pair_align 1.3.12 [tarball] — that's the source slash version, straight from the tarball, and the man page lives under the PAIR_ALIGN(1) banner. anyway ily, go align something, you're gonna do amazing. bye bestie 💜✨🎀