TREEANNOTATOR2(1)

📦 version 2.7.8, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 TREEANNOTATOR2(1) — the treeannotator2 glow-up 💖

okay bestie, sit down, hydrate, and let me tell you about treeannotator2(1) — she's part of the beast2 package and she is, and I say this with my whole chest, that girl. 🦋

✨ NAME ✨

treeannotator2 — MCMC output analysis of the beast2 package. no cap, that's literally her whole job description and she ate. 💅

🎀 SYNOPSIS 🎀

treeannotator [-heights <keep|median|mean|ca>] [-burnin <i>] [-b <i>]
[-limit <r>] [-target <target_file_name>] [-help] [-forceDiscrete]
[-lowMem] [-hpd2D <r>] <input-file-name> [<output-file-name>]

yes she's invoked as treeannotator even though the page says treeannotator2. that's just her government name vs. her name-name. iykyk. 🙈

🌸 DESCRIPTION 🌸

so. BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. bestie she is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. like, that's her whole personality and honestly? iconic.

she can be used as a method of reconstructing phylogenies, but she's also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. the way that she uses MCMC to average over tree space so that each tree is weighted proportional to its posterior probability… no notes, genuinely. 🌈

also included: a simple to use user-interface program for setting up standard analyses, plus a suit of programs for analysing the results. very much giving "i contain multitudes." 👑

one thing you need to know though: this treeannotator version matches beast2-mcmc, which is no new upstream version of beast-mcmc (1.x) — it's rather a rewritten version. so don't come for her thinking she's a glow-up of the old one, she's a whole different era. periodt. 💀

💅 OPTIONS 💅

  • -heights — an option of 'keep' (default, bestie, remember this one), 'median', 'mean' or 'ca'. pick your fighter. 🥊
  • -burnin — the percentage of states to be considered as 'burn-in'. yes, we're burning the beginning, that's the vibe.
  • -b — the percentage of states to be considered as 'burn-in'. same energy as -burnin, just shorter. she's the low-effort twin. 👯
  • -limit — the minimum posterior probability for a node to be annotated. if a node doesn't clear the bar, she's not getting her little label. sorry to that node. 🙈
  • -target — specifies a user target tree to be annotated. you bring the tree, she does the annotating. that's the arrangement. 🫶
  • -help — option to print this message. she will simply tell you about herself. main character energy, honestly. ✨
  • -forceDiscrete — forces integer traits to be treated as discrete traits. no arguments, she just does it. 💪
  • -lowMem — use less memory, which is a bit slower. trade-off queen. your RAM will thank you, your clock will not. 😭
  • -hpd2D — the HPD interval to be used for the bivariate traits. two traits, one interval, very demure. 🎀

🔥 EXAMPLES 🔥

here's how you actually run her, bestie:

treeannotator2 test.trees out.txt
treeannotator2 -burnin 10 -heights mean test.trees out.txt
treeannotator2 -burnin 20 -target map.tree test.trees out.txt

copy, paste, slay. ⭐

💜 AUTHOR 💜

this manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. shoutout Andreas, we love a documenter. 🫶

okay and that's the whole page!! this was treeannotator2 2.4.1, dated May 2016 — yes bestie she's a vintage, she's aged like a fine wine, we stan a legacy queen. go annotate some trees and text me when you're done. bye!! 💖🧚🌸

📦 where this page comes from