NCLCONVERTER(1)

🎀 NAME 🎀

Okay bestie, welcome to the NCLCONVERTER(1) manual 💖 It's a User Commands page and I am so obsessed 😭

NCLconverter is a report of the content of a NEXUS file 🦋

💜 DESCRIPTION 💜

So NCLconverter reads a file 📖 and writes a report of what's inside it. The report goes to a file prefix you pick with -o, in the output format you pick with -e. Lowkey iconic, honestly ✨

The most common usage is literally just this:

NCLconverter <path to NEXUS file>

🌸 OPTIONS 🌸

• -h — type this on the command line and it shows the help message 💅
• -q — quiets 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, which means 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 instead. This should not be used with NEXUS files 💀
• -s<non-negative integer> — controls the NEXUS strictness level 🔥
  • The default level is equivalent to -s2.
  • Invoking with -s3 or higher turns some warnings into fatal errors.
  • Running with -s1 makes the parser accept dangerous constructs.
  • Running with -s0 makes the parser try every single way to finish parsing the file, warning about very serious errors along the way.

Note: when the -s0 strictness level is used and the parser fails to finish, the cause is often an earlier error, not the one in the last message. Keep that in mind, bestie 🙈

• -i<number> — sets the length of the interleaved pages to create 📏
• -f<format> — specifies the input file format you expect 🧚
  • -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

• -e<format> — specifies the output file format you expect 📤
  • -enexus — "normalized" NEXUS output ✨
  • -efasta — character data in fasta. This could result in multiple output files 🧩
  • -ephylip — trees and character data in phylip. This could result in multiple output files 🌳
  • -erelaxedphylip — trees and character data in relaxed phylip. This could result in multiple output files 🌿
  • -enexml — nexml output (this is also the default) 💜
• -o<fn> — specifies the output prefix. An appropriate suffix and extension get added on for you 🏷️
• -d<fn> — specifies the single output destination. You can also use -d- to send the output to standard output 📺

Warning: using this option may result in invalid output, because separate "blocks" of information get concatenated into a single file!

• -u — converts underscores to spaces in formats other than NEXUS 🫧
• -y<filename> — translates to "safe" taxon names and stores the new names as a NEXUS file called <filename> with a TaxaAssociation block. The first taxa block in the association block holds the original names, and the second holds the "safe" names 🔐
• -Y<filename> — behaves like -y, except a translation file gets produced even if the original names were already "safe" 🔁
• -z<filename> — uses the NEXUS-formatted file called <filename> with a TaxaAssociation block to restore the original names. It assumes the first taxa block in the TaxaAssociation block holds the original name and the second holds the current name. This is super useful for "undoing" the effects of the -y option 🪄
• -j — suppresses the creation of a NameTranslationFile 🙈

👑 AUTHOR 👑

Andreas Tille wrote this manpage for the Debian distribution 🧚 and it can be used for any other usage of the program 🫶

That's the whole tea ☕ Stay iconic, bestie 💅✨ NCLconverter 2.1.18, January 2016, NCLCONVERTER(1) 🎀💖