alignment-max(1)

🎀 NAME 🎀

okay bestie, meet alignment-max (aka alignment-max(1)) 💅 it's giving: construct a posterior decoding alignment that summarizes an alignment sample ✨

---

🦋 SYNOPSIS 🦋

alignment-max [OPTIONS] < alignments-file

---

🌸 DESCRIPTION 🌸

ngl this is the main vibe: it builds a posterior decoding alignment so you can summarize a whole alignment sample in one go 🫶

---

💖 ALLOWED OPTIONS: 💖

• -h, –help — shows you the help message 🙈
• –alphabet arg — picks your alphabet: DNA, RNA, Amino-Acids, Amino-Acids+stop, Triplets, Codons, or Codons+stop 🧬
• -s arg (=0), –skip arg (=0) — how many alignment samples to skip ⏭️
• -m arg (=1000), –max-alignments arg (=1000) — max number of alignments to analyze 📊
• –analysis arg (=multiply) — pick one of sum, wsum, wsum2, or multiply 🔥
• –column-pr arg (=homology) — pick homology or alignment 🌈
• -S arg (=1), –sort arg (=1) — sorts partially ordered columns so similar gaps end up grouped together 🍓
• -o arg (=-), –out arg (=-) — output file, and if you don't pick one it goes to stdout 💜
• -p arg, –out-probabilities arg — output file for column probabilities, but only if you specify it 🧚
• –debug-graph arg — filename for the debug graph 🕵️‍♀️
• -V, –verbose — extra log messages on stderr, for when you need the tea ☕

---

🚨 REPORTING BUGS: 🚨

bestie if something's broken, here are the receipts 💀

the BAli-Phy online help lives at http://www.bali-phy.org/docs.php 🌐

send bug reports to bali-phy-users@googlegroups.com 💌

---

👑 AUTHORS 👑

written by Benjamin Redelings ✨ the real MVP 🫶

---

That's the whole page, bestie 🌈💖 last updated Feb 2018, and it's still giving 💅✨