NEXUSVALIDATOR(1)

📦 version 2.1.21+git20210811.b1213a7, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

Hiii bestie 💖 this is the manual page for NEXUSvalidator, section 1 (User Commands) 🎀

✨ NAME ✨

NEXUSvalidator — validate NEXUS file 🌸

💅 DESCRIPTION 💅

Okay so NEXUSvalidator reads a file and exits with a success (return code 0) if the file is valid ✅ it's giving clean energy 🫶

The most common usage is simply:

NEXUSvalidator <path to NEXUS file>

🌈 OPTIONS 🌈

  • -h — pop it on the command line and it shows this help message 💁‍♀️
  • -q — shush the NCL status messages while files are being read 🤫
  • -l<path> — reads a file and treats every line in it 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-non-negative integer> — controls the NEXUS strictness level 🎚️
    • the default level is equivalent to -s2
    • -s3 or a higher number converts some warnings into fatal errors 💀
    • -s1 makes the parser accept dangerous constructs ⚠️
    • -s0 makes the parser 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's often the result of an earlier error than the one reported in the last message 😭
  • -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 🫶

That's the whole page, bestie 🧚 this one is from NEXUSvalidator 2.1.18, dated January 2016 💜 stay valid, you're iconic 💅✨

📦 where this page comes from