JALIGNER(1)

okay so bestie, welcome to the JALIGNER(1) manual page — section 1, obviously — and it's literally the Smith-Waterman algorithm with Gotoh's improvement. no cap, this is the sequence alignment serve. 💖

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✨ NAME ✨

jaligner — Smith-Waterman algorithm with Gotoh's improvement. that's the whole name, it's giving bioinformatics royalty. 👑

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🌸 SYNOPSIS 🌸

jaligner <s1> <s2> <matrix> <open> <extend>

Or just type jaligner to see the GUI.

so if you're a CLI girly, you pass in <s1>, <s2>, <matrix>, <open>, and <extend>. and if you just type jaligner with no args? boom, GUI. main character energy fr fr. 🦋

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🎀 EXAMPLES 🎀

jaligner p53_{human,mouse}.fasta BLOSUM62 10 0.5

like, look at that brace expansion — p53_{human,mouse}.fasta is lowkey a flex. BLOSUM62 matrix, open 10, extend 0.5, and you're off. slay. 💅

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🦋 HOMEPAGE 🦋

http://jaligner.sourceforge.net/

that's the link, bestie. go peek. ✨

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and that's the jaligner(1) manual page, section 1 — the footer just says JALIGNER(1) again, no version or date listed, but honestly? still iconic. stay slaying, and remember: every single flag and detail from the original is right here, periodt. 🫶🌸💜