NJPLOT(1)

📦 version 2.4, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 NJPLOT 💖

okay bestie, sit down, hydrate, and let me tell you about njplot — it's a phylogenetic tree drawing program for biologists, and honestly? it's giving main character energy in the tree-drawing department. 🌳✨

This page lives in the General Commands Manual section, and it's the glow-up version of njplot, newicktops, and newicktotxt all in one. 🫶

✨ SYNOPSIS ✨

njplot [options] tree_file

newicktops [options] tree_file

newicktotxt [options] tree_file

three whole commands, one little family. slay. 💅

🌸 DESCRIPTION 🌸

so this manual page documents briefly the njplot command. brief but iconic, yk?

The newicktops command does exactly the same but needs no X11 display — like, zero display, zero drama. The output is rendered into a PostScript file instead.

The newicktotxt command does exactly the same as newicktops but the output is rendered into a text file. same vibe, different font of delivery, fr fr.

real talk: this manual page was rewritten for the Debian GNU/Linux distribution because the original program does not have a manual page. we did it for the culture. 😭

njplot is a tree drawing program able to draw any binary or multi-branched tree expressed in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. bestie it literally specializes in that. no cap. 🔥

Any rooting of the unrooted tree can be interactively specified using the mouse. 🖱️ NJplot also allows zooming, branch swapping, display of bootstrap scores and saving in the PostScript format. NJplot can therefore be used as a graphical extension of any package of phylogenetic program which employs the standard tree format for storing trees (i.e., with most such packages). the way it just slots into your whole workflow?? obsessed. 👑

💅 OPTIONS 💅

okay so there are only the following options, and lowkey important: they only work in an x-terminal-emulator, but not in console mode. read that again. i'll wait. 🫶

  • -h — prints out brief help. your little emergency SOS, but make it helpful. 🙈
  • -us — PostScript tree file prepared for US Letter paper size. america's finest, paper-wise. 🇺🇸
  • -psonly — no window interface, just write the PostScript tree file. ghost mode activated. 👻
  • -size n — font size n used for taxon names. your names, your size, your rules. ✨
  • -pc n — number of pages for PostScript output. because sometimes one page simply isn't enough room for the lore. 📄📄
  • -psize widthxheight — size of PostScript page expressed as WIDTHxHEIGHT. yes, with the little x in the middle, exactly like that. 📐
  • -lengths — show branch lengths if they appear in tree file. only if they appear, bestie. we don't manifest data that isn't there. 🦋
  • -boot — show bootstrap values if they appear in tree file. same energy, same rule. 🎀
  • -notitle — don't include title in PostScript output. minimalism. the title said "not today." 💀

🔍 SEE ALSO 🔍

Word-Wide-Web: 🌐

http://pbil.univ-lyon1.fr/software/njplot.html

👑 AUTHOR 👑

Manolo Gouy e-mail: mgouy@biomserv.univ-lyon1.fr

This manual page was written by Dr. Guenter Bechly <gbechly@debian.org>, for the Debian GNU/Linux system (but may be used by others). generous queen behavior, honestly. 💜

and that's the whole page, bestie! this one came to you from the General Commands Manual, dated April 10, 2001 — yes, a vintage icon, we stan a timeless slay. 🌈⭐ go draw some trees. 🌳💖

📦 where this page comes from