MLAGAN(1)

💖 MLAGAN(1) — the user commands era 💖

okay bestie, sit DOWN, because today we're talking about mlagan, and this one is a highly parametrizable pairwise global aligner ✨ it lives in section 1 of the manual, iykyk.

🌸 NAME 🌸

mlagan — a highly parametrizable pairwise global aligner. that's it, that's the whole vibe. no cap. 💅

🎀 SYNOPSIS 🎀

mlagan seqfile_1 seqfile_2 [... seqfile_63] [-parameters]

yes bestie, up to 63 sequence files. sixty-three. she's ambitious and we respect it. 👑

🦋 DESCRIPTION 🦋

so here's the tea 🍓 — Lagan takes the local alignments that CHAOS generated, uses them as anchors, and then limits the search area of the Needleman-Wunsch algorithm around those anchors. she's not searching the whole world, she's searching around the anchors, and honestly? efficient queen. 💅

Multi-LAGAN is a generalization of the pairwise algorithm to multiple sequence alignment. M-LAGAN does progressive pairwise alignments, guided by a user-specified phylogenetic tree 🌳 and then alignments get aligned to other alignments using the sum-of-pairs metric. alignments aligning with alignments. it's giving community. it's giving support system. 🫶

✨ OPTIONS ✨

bestie heads up: this list appears twice in the original. not a typo on my part, I'm keeping it exactly as she wrote it. twice the options, twice the love. 💀💖

• -nested — runs improvement in a nested fashion 🪆
• -postir — incorporates the final improvement phase
• -lazy — uses lazy mode 😴 (she's resting but she's still working, iconic)
• -translate — use translated anchors
• -fastreject — use fast rejection (tuned for human/mouse or closer) 🐭
• -verbose — give debug output 🗣️
• -tree "(...)" — runs with given phylogenetic tree 🌳
• -out "filename" — outputs to filename 📝
• -nucmatrixfile "filename" — uses given substitution matrix instead of $LAGAN_DIR/nucmatrix.txt 🔄
• -version — prints version info 🏷️

and now, again, because she said it twice:

• -nested — runs improvement in a nested fashion 🪆
• -postir — incorporates the final improvement phase
• -lazy — uses lazy mode 😴
• -translate — use translated anchors
• -fastreject — use fast rejection (tuned for human/mouse or closer) 🐭
• -verbose — give debug output 🗣️
• -tree "(...)" — runs with given phylogenetic tree 🌳
• -out "filename" — outputs to filename 📝
• -nucmatrixfile "filename" — uses given substitution matrix instead of $LAGAN_DIR/nucmatrix.txt 🔄
• -version — prints version info 🏷️

🌈 ENVIRONMENT 🌈

the LAGAN_DIR variable specifies the location of the nucmatrix file. it defaults to /usr/lib/lagan, which is also where Debian places that file. so if you were wondering where your nucmatrix went... she's at /usr/lib/lagan, bestie. mystery solved. 🔍✨

⚠️ quick note, no drama: that $LAGAN_DIR default is literally where Debian puts the file, so if you've moved it or you're on a different setup, check before you assume. 🫶

and that's the whole page, my love 💜 written by mlagan, dated September 2018, hanging out in the MLAGAN(1) section of the manual — stay aligned, stay anchored, and don't forget to set your LAGAN_DIR. periodt. 👑✨🎀