PREPAREALIGN(1)

💖 PREPAREALIGN(1) 💖

okay bestie, welcome to the prepareAlign page — yes, that's the manual for section 1, we're in the big leagues now ✨

✨ NAME ✨

prepareAlign — get an alignment ready for block profile creation by yeeting the gap-rich rows 🗑️💅

🌸 SYNOPSIS 🌸

prepareAlign < input.fa  > output.fa

🦋 DESCRIPTION 🦋

so like, you feed it a multiple alignment of proteins through standard input. prepareAlign then removes rows from that alignment, and the whole goal here is to end up with fully conserved blocks in whatever alignment is left over — and that alignment gets written out to standard output. no cap. 👑

now here's the situation, and it's giving struggle. when an alignment has a ton of sequences and way too many gaps — think a whole full PFAM alignment, like, the entire thing, bestie 😭 — and you try to run msa2prfl.pl, it just hits you with:

"No blocks found in MSA"

which is the computational equivalent of "no thoughts, head empty" 💀 so when that happens? you run prepareAlign first to eliminate sequences. that's the move. that's the whole vibe. 🌈

👑 AUTHORS 👑

Oliver Keller

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and that's a wrap, gorgeous 🫶 this was the PREPAREALIGN(1) page, so take that manual name with you — now go delete some gap-rich rows and make those blocks fully conserved, mwah 💖🎀