NEXUSNORMALIZER(1)

✨ NEXUSNORMALIZER(1) ✨ 🎀

okay so bestie, this is the NEXUSnormalizer manual, and it's giving tidy-up energy 💅 — it's a whole vibe for making NEXUS files look clean and consistent 🫶

💖 NAME

NEXUSnormalizer — rewrites a NEXUS file to standard out with consistent indentation and syntax ✨

🦋 SYNOPSIS

NEXUSnormalizer <path to NEXUS file>

🌸 DESCRIPTION

okay so NEXUSnormalizer takes a file, reads it, and rewrites it to standard out with consistent indentation and syntax. literally that's the whole main character moment 👑

The most common usage is simply:

NEXUSnormalizer <path to NEXUS file>

💜 OPTIONS

• -h — on the command line, this shows the help message 🧚
• -q — suppresses NCL status messages while reading files 🤫
• -l<path> — reads a file and treats each line of that file as a path to a NEXUS file 🗂️
• -a — outputs AltNexus (no translation table in trees) 🌈
• -x — do NOT validate internal labels in trees as taxa labels 🙅‍♀️
• -X — do NOT treat numbers in trees as taxon numbers; treat them as arbitrary labels (should not be used with NEXUS files) ⚠️
• -s<non-negative integer> — controls the NEXUS strictness level 🎚️

The default level is equivalent to -s2. Invoking the program with -s3 or a higher number will convert some warnings into fatal errors. Running with -s1 will cause the parser to accept dangerous constructs, and running with -s0 will cause the parser to make every attempt to finish parsing the file (warning about very serious errors).

⚠️ Note that when the -s0 strictness level is used and the parser fails to finish, it will often be the result of an earlier error than the error that is reported in the last message. bestie, read up the file, not just the last line 😭

• -i<number> — specifies the length of the interleaved pages to create 📄
• -f<format> — specifies the input file format expected 📥
  • -fnexus — NEXUS (this is also the default) 💕
  • -faafasta — amino acid data in fasta 🧬
  • -fdnafasta — DNA data in fasta 🧬
  • -frnafasta — RNA data in fasta 🧬

The complete list of format names that can follow the -f flag is:

• nexus
• dnafasta
• aafasta
• rnafasta
• dnaphylip
• rnaphylip
• aaphylip
• discretephylip
• dnaphylipinterleaved
• rnaphylipinterleaved
• aaphylipinterleaved
• discretephylipinterleaved
• dnarelaxedphylip
• rnarelaxedphylip
• aarelaxedphylip
• discreterelaxedphylip
• dnarelaxedphylipinterleaved
• rnarelaxedphylipinterleaved
• aarelaxedphylipinterleaved
• discreterelaxedphylipinterleaved
• dnaaln
• rnaaln
• aaaln
• phyliptree
• relaxedphyliptree
• nexml
• dnafin
• aafin
• rnafin

🎀 AUTHOR

this manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program 🫶

okay that's the tea, bestie 🍓 manual by Andreas Tille, NEXUSnormalizer 2.1.18, January 2016 — now go normalize something and slay 💅✨