alignment-indices(1)

✨ NAME ✨

Okay bestie, the tool is alignment-indices 🦋 and its whole job is to show the alignment in terms of the index of each character in its sequence. Main character energy, no cap 💅

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🧚 SYNOPSIS 🧚

alignment-indices alignment-file [OPTIONS]

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🌸 DESCRIPTION 🌸

Lowkey simple but highkey iconic: it shows the alignment by giving you the index of every character in its sequence 😭✨

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👑 ALLOWED OPTIONS: 👑

• -h, –help — pulls up the help message 🫶
• –align arg — point it at the file with your sequences and initial alignment 🍓
• –alphabet arg — set it to Codons' if you want codon alphabets preferred 🧬
• -c arg, –columns arg — choose which ranges of columns to keep, like 1-10,30- 🎀
• –invariant arg — only print sites where this site and arg neighbors are invariant 💖
• –differences arg — how many sequences are allowed to differ from the majority? 🤔
• –avoid-gaps arg (=3) — how far from a gap does a column have to be before it counts as invariant? 🌈
• –min-constraints arg — the minimum # of constraints per column needed for a constraint to get emitted 💜

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🐛 REPORTING BUGS: 🐛

Stuck or spotted something weird? BAli-Phy's online help is at http://www.bali-phy.org/docs.php 📚

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

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🎀 AUTHORS 🎀

The genius behind it all is Benjamin Redelings 👑

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Okay that's the whole tea, bestie 🦋 this page was last updated in Feb 2018, and the manual is alignment-indices(1) forever 💅💖