alignment-consensus(1)

🎀 NAME 🎀

Okay bestie, welcome to the manual page for alignment-consensus(1) 💖 It's giving tidy and useful. So alignment-consensus is the tool that builds a consensus alignment to summarize an alignment sample 🧬✨

🧚 SYNOPSIS 🧚

alignment-consensus alignments-file [alignments-file ...]  [OPTIONS]

🌸 DESCRIPTION 🌸

Ngl, the whole job is to construct a consensus alignment that sums up an alignment sample. Main character energy 👑

💅 ALLOWED OPTIONS 💅

• -h, –help — pulls up the help message 🫶
• –alphabet arg — pick 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, default 0 🦋
• -m arg (=1000), –max arg (=1000) — the max number of alignments to analyze, default 1000 🔥
• –strict arg — ignore events below this probability 🙈
• –cutoff arg — also ignore events below this probability, same vibe as –strict 🌈
• –uncertainty arg — the file name for AU uncertainty vs level 📄
• –chop-to arg — keep only the first arg taxa ✂️
• -V, –verbose — gives you more log messages on stderr 🍓

🙈 REPORTING BUGS 🙈

Bestie, if you're stuck, the BAli-Phy online help is at http://www.bali-phy.org/docs.php 📚

And if something's broken, send your bug reports to bali-phy-users@googlegroups.com 💌

👑 AUTHORS 👑

Benjamin Redelings. The real OG 💜

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That's the Feb 2018 version of alignment-consensus(1) for you, bestie 💖 Stay iconic and keep those alignments slaying 💅✨