alignment-gild(1)

Heyy bestie 💖 okay so let's talk about alignment-gild(1) 🦋 it's the tool that gives every residue in your alignment a little grade for how likely it is to line up with the imaginary root character in its column ✨

🌸 NAME 🌸

okay so the name is alignment-gild, and it's giving annotation queen 👑 It annotates each residue in the alignment based on the probability that it should align to the hypothetical root character in its column 🫶

🧚 SYNOPSIS 🧚

alignment-gild alignment-file tree-file alignments-file
[alignments-file] [OPTIONS]

🎀 DESCRIPTION 🎀

so basically it slaps an annotation on every residue in the alignment 💅 the score tells you how probable it is that the residue should line up with the imaginary root character sitting in its column 🌈

💜 ALLOWED OPTIONS 💜

• -h, –help — pulls up the help message 🆘
• –align arg — the file with the alignment you want annotated 📄
• –tree arg — the file with the tree 🌳
• –find-root — estimates the root position from the branch lengths 🧭
• –alphabet arg — set it to Codons' if you want codon alphabets preferred 🧬
• –skip arg (=0) — the number of alignment samples to skip, defaulting to =0 🙈
• –max-alignments arg (=1000) — the max number of alignments to analyze, defaulting to =1000 🔥
• -V, –verbose — outputs more log messages on stderr 🔊

🦋 REPORTING BUGS 🦋

if something's acting sus, the BAli-Phy online help lives at http://www.bali-phy.org/docs.php 💻

and for bug reports, send them to bali-phy-users@googlegroups.com 📬 the devs will be so grateful, no cap 🫶

👑 AUTHORS 👑

the iconic author is Benjamin Redelings 🌟

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that's the tea from alignment-gild(1), last updated Feb 2018 💅🌸 go be a main character in your alignments, bestie! 💖🧚