PRANK(1)

💅 PRANK(1) — The Probabilistic Alignment Kit 🧬

okay bestie, sit down, hydrate, and let me tell you about prank, which lives in section 1 of the manual (that's the "user commands" section, iykyk) and comes to you straight from The Probabilistic Alignment Kit. Yes the name is funny. Yes it's actually a whole multiple sequence aligner. Both things are true. 🌸

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✨ NAME ✨

prank — Computes probabilistic multiple sequence alignments. that's it, that's the job, and it ate. 👑

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🌈 SYNOPSIS 🌈

prank sequence_file

prank [optional parameters] -d=sequence_file [optional parameters]

so either you hand it a sequence_file and vibe, or you go full -d= mode with as many optional parameters as your heart desires. main character energy either way. 🫶

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💖 DESCRIPTION 💖

The Probabilistic Alignment Kit (aka PRANK, aka your new fave) is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. it's built on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. like, it actually understands what an insertion is. we love a program with emotional intelligence. 😭✨

plus, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the evolutionary distances between sequences. it's giving "learned from the best, did it better." 🔥

and lastly — the iconique part — PRANK lets you define a potential structure for the sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences. multitasking queen behavior, no cap. 💅

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🎀 OPTIONS 🎀

🦋 INPUT/OUTPUT PARAMETERS 🦋

• -d=sequence_file — the input sequence file, in FASTA format. your raw material, bestie. 🍓
• -t=tree_file — the tree file to use. if you leave it unset, an appriximated NJ tree is generated for you. 🧚
• -o=output_file — sets the name of the output file. if unset, output_file is set to output. default naming, we love a low-effort moment. ✨
• -f=output_format — sets the output format. output_format can be one of fasta (default), phylipi, phylips, paml, or nexus. pick your aesthetic. 🌈
• -m=model_file — the model file to use. if unset, model_file is set to HKY2/WAG. 💜
• -support — compute posterior support.
• -showxml — output alignment xml-file.
• -showtree — output alignment guidetree.
• -showanc — output ancestral sequences. yes, the ancestors. we're doing genealogy. 👑
• -showall — output all of these. the whole bundle. slay.
• -noanchors — do not use Exonerate anchoring. (Exonerate has to be installed separately, so this is very much a you problem, bestie.) 🫶
• -nomafft — do not use MAFFT for guide tree. (MAFFT also has to be installed separately. same deal.) 💀
• -njtree — estimate tree from an input alignment (and realign). it's a glow-up for your alignment, fr fr.
• -shortnames — truncate names at first space character. bye bye, extra words. ✂️
• -quiet — reduce output. for when the terminal is being too loud. 🙈

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🌸 ALIGNMENT MERGE 🌸

merging two alignments together? romantic. 🥰

• -d1=alignment_file — the first input alignment file, in FASTA format.
• -d2=alignment_file — the second input alignment file, in FASTA format.
• -t1=tree_file — the tree file for the first alignment. if unset, an appriximated NJ tree is generated. 🌱
• -t2=tree_file — the tree file for the second alignment. if unset, an appriximated NJ tree is generated. 🌱

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⭐ MODEL PARAMETERS ⭐

• -F, +F — force insertions to be always skipped. absolutely no insertions allowed, periodt.
• -gaprate=# — set the gap opening rate. default is 0.025 for DNA and 0.005 for proteins.
• -gapext=# — set the gap extension probability. default is 0.75 for DNA and 0.5 for proteins.
• -codon — use empirical codon model for coding DNA.
• -DNA, -protein — use the DNA or protein model, respectively. this disables auto-detection of model, so choose wisely bestie. 👀
• -termgap — penalise terminal gaps normally.
• -nomissing — no missing data. use -F for terminal gaps. (they're telling you the combo, take the hint 💅)
• -keep — do not remove gaps from pre-aligned sequences. protect the gaps. they were there for a reason. 🛡️

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💜 OTHER PARAMETERS 💜

• -iterate=# — rounds of re-alignment iteration. by default, it iterates five times and keeps the best result. it's not indecisive, it's thorough. 😌
• -once — run only once. same as -iterate=1.
• -prunetree — prune guide tree branches with no sequence data. ✂️🌳
• -prunedata — prune sequence data with no guide tree leaves. ✂️🧬
• -uselogs — slower but should work for a greater number of sequences.
• -translate — translate input data to protein sequences.
• -mttranslate — translate input data to protein sequencess using mt table. (yes, sequencess. the source said it, I said it, we all move on together. 💀)
• -convert — do not align, just convert to a different format. sometimes you just need a wardrobe change. 👗
• -dna=dna_sequence_file — DNA sequence file for backtranslation of protein alignment.
• -help — show an extended help page with more options. yes, there are more. iconic.
• -version — show version and check for updates.

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👑 AUTHORS 👑

prank was written by Ari Loytynoja. 💖

this manual page was originally written by Manuel Prinz <manuel@debian.org> for the Debian project (and may be used by others). we stan a generous king. 🫶

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reminder bestie: every flag, every default, every number up there is load-bearing. don't freestyle with -gaprate=# unless you mean it. 😭

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and that's the whole page!! this is from v.121211, dated 2025-09-08, and it was served to you by PRANK(1) — the section 1 girlies. now go align something beautiful. mwah. 💅✨🎀🦋💖