MSA_DIFF(1)

✨ NAME ✨

msa_diff — compare two multiple alignments and report the differences 💖

🌸 DESCRIPTION 🌸

okay so bestie, picture this: you've got two multiple alignments and you're sitting there like "are these actually the same or am i losing it" 🙈 msa_diff is literally the friend who looks at both of them and tells you exactly what's different. compare two multiple alignments, report the differences. that's the whole vibe. no cap. 🦋

💅 OPTIONS 💅

• --format1, -i _FASTA|SS|PHYLIP|MPM|MAF_ — the format of the first alignment. if you don't say anything, it lowkey just guesses by peeking at the file contents 👀 (default is to guess format from file contents).
• --format2, -j _FASTA|SS|PHYLIP|MPM|MAF_ — same energy, but for the second alignment. also defaults to guessing from the file contents ✨
• --alphabet, -a _<alphabet_string>_ — use the string you give it as the alphabet. this one's for when your data is a lil nonstandard and you need to make room for it, like 'b' for any base, or '^' for insertion gaps, or '.' for deletion gaps. accommodating your weird characters, iconic behavior 🫶
• --ignore-base-id, -b — ignore the identity of the bases. basically it treats every alphabetical character as equivalent, so like A, C, G, T, N, X, b all get read as "a base, whatever" 💀 all bases are valid and we don't discriminate.
• --ignore-gap-type, -g — ignore what kind of gap it is. '-', '^', and '.' all count as the same thing. a gap is a gap, periodt 💅
• --help, -h — show this help message and dip. that's it, that's the option 👑

fr fr tho, if you're comparing alignments and the only thing bugging you is that one file calls gaps '^' and the other calls them '.', bestie that's not a real problem, that's a -g problem 🌈

and that's the whole page, babe 💜 this was msa_diff 1.4, living its best life since May 2016, and yeah, it's a User Commands moment — go diff some alignments, you've got this 🎀