PAL2NAL.PL(1)

💖 NAME 💖

okay so welcome to the PAL2NAL.PL(1) page, bestie — User Commands section, very demure, very mindful 💅

pal2nal.pl — use insight from protein alignment for nucleotide alignment. that's the whole vibe. protein tea → nucleotide glow-up ✨

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✨ SYNOPSIS ✨

pal2nal.pl pep.aln  nuc.fasta  [nuc.fasta...]  [options]

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🌸 DESCRIPTION 🌸

pal2nal.pl (v13) 🫶

🧬 pep.aln

protein alignment, either in CLUSTAL or FASTA format. pick your fighter, both are valid 💖

🍓 nuc.fasta

DNA sequences — either one single multi-fasta, or separate files, your call queen 👑

💅 Options

• -h — show help. literally just help. we love a supportive icon ✨
• -output (clustal|paml|fasta|codon) — the output format you want; default = clustal 💖
• -blockonly — shows only the user specified blocks '#' under the CLUSTAL alignment (peep the example, iykyk) 👀
• -nogap — removes columns with gaps and inframe stop codons. like, bye 🧹
• -nomismatch — removes mismatched codons (that's a mismatch between pep and cDNA) from the output 🙈
• -codontable (universal|vmitochondria) — the codon table, bestie:
  • universal (default)
  • vmitochondria -> vertebrate mitochondrial 🦋
• -html — HTML output (only for the web server) 🌈
• -nostderr — no STDERR messages (only for the web server) 🤫

also important, no cap: the sequence order in pep.aln and nuc.fasta should be the same. like, matching order. please. 🙏

and: the IDs in pep.aln are used in the output. periodt 👑

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🔁 DESCRIPTION (the sequel, not me repeating myself but the page literally does)

okay so the original page says all of this twice and we're keeping every single crumb of it, so here we go again, bestie 💀✨

pal2nal.pl (v13)

Usage: pal2nal.pl pep.aln nuc.fasta [nuc.fasta...] [options]

🧬 pep.aln

protein alignment, either in CLUSTAL or FASTA format 💖

🍓 nuc.fasta

DNA sequences (single multi-fasta or separated files) 🌸

💅 Options

• -h — show help ✨
• -output (clustal|paml|fasta|codon) — output format; default = clustal 🎀
• -blockonly — show only user specified blocks '#' under CLUSTAL alignment (see example) 👀
• -nogap — remove columns with gaps and inframe stop codons 🧹
• -nomismatch — remove mismatched codons (mismatch between pep and cDNA) from the output 🙈
• -codontable (universal|vmitochondria) — codon table:
  • universal (default)
  • vmitochondria -> vertebrate mitochondrial 🦋
• -html — HTML output (only for the web server) 🌈
• -nostderr — no STDERR messages (only for the web server) 🤫

reminder bestie: sequence order in pep.aln and nuc.fasta should be the same 🫶

and the IDs in pep.aln are used in the output 💅

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👑 SEE ALSO 👑

the full documentation for pal2nal.pl is maintained as a Texinfo manual. if the info and pal2nal.pl programs are properly installed at your site, the command

info pal2nal.pl

should give you access to the complete manual. slay, go read it 📚✨

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and that's the whole page, bestie — this was pal2nal.pl, PAL2NAL.PL(1), dated November 2010 💖 no cap, that's the sign-off, mwah 🫶🎀