BEAST2-MCMC(1)

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

💖 BEAST2-MCMC 💖

okay bestie, you found the manual for beast2-mcmc (that's the BEAST2-MCMC(1) page, for the record, so you know exactly where you are 🫶) — it's the command-line side of BEAST2, and we are gonna go through every single flag together. no skimming. we don't do that here. ✨

🌸 NAME 🌸

beast2-mcmc — Bayesian MCMC phylogenetic inference 🦋

✨ SYNOPSIS ✨

beast2-mcmc [-window] [-options] [-working] [-seed] [-prefix <PREFIX>]
[-statefile <STATEFILE>] [-overwrite] [-resume] [-validate] [-errors
<i>] [-threads <i>] [-java] [-noerr] [-loglevel <LEVEL>] [-instances
<i>] [-beagle] [-beagle_info] [-beagle_order <order>] [-beagle_CPU]
[-beagle_GPU] [-beagle_SSE] [-beagle_single] [-beagle_double]
[-beagle_scaling <default|none|dynamic|always>] [-help] [-version]
[<input-file-name>]

like… yes, it's a lot of brackets. breathe. we'll get to each one. 🧚

👑 DESCRIPTION 👑

so BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. cross-platform means it does not care what machine you're on, it will simply slay everywhere. 💅

it's entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. that's the whole vibe. it can be used as a method of reconstructing phylogenies, but it's also a framework for testing evolutionary hypotheses without conditioning on a single tree topology — so no being loyal to one tree, we're averaging, we're free. 🌈

BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. literally each tree gets its moment proportional to how likely it is. iconic behaviour honestly.

also included: a simple to use user-interface program for setting up standard analyses, and a suit of programs for analysing the results. ✨

not me needing to say this, but: this is no new upstream version of beast-mcmc (1.x) but rather a rewritten version. so don't come at it expecting the 1.x lore, bestie, it's a whole different era. 💀

💅 OPTIONS 💅

one bullet per flag, all of them, no cap:

  • -window — provide a console window 🪟
  • -options — display an options dialog
  • -working — change working directory to input file's directory
  • -seed — specify a random number generator seed 🎲
  • -prefix — specify a prefix for all output log filenames
  • -statefile — specify the filename for storing/restoring the state
  • -overwrite — allow overwriting of log files
  • -resume — allow appending of log files
  • -validate — parse the XML, but do not run — useful for debugging XML 🐛
  • -errors — specify maximum number of numerical errors before stopping
  • -threads — the number of computational threads to use (default 1), -1 for number of cores 🔥
  • -java — use Java only, no native implementations
  • -noerr — suppress all output to standard error
  • -loglevel — error,warning,info,debug,trace
  • -instances — divide site patterns amongst number of threads (use with -threads option)
  • -beagle — use beagle library if available 🐶
  • -beagle_info — BEAGLE: show information on available resources
  • -beagle_order — BEAGLE: set order of resource use
  • -beagle_CPU — BEAGLE: use CPU instance
  • -beagle_GPU — BEAGLE: use GPU instance if available
  • -beagle_SSE — BEAGLE: use SSE extensions if available
  • -beagle_single — BEAGLE: use single precision if available
  • -beagle_double — BEAGLE: use double precision if available
  • -beagle_scaling — BEAGLE: specify scaling scheme to use
  • -help — print this information and stop 🛑
  • -version — print version and stop
quick lil heads up: the synopsis is where the args live, so -prefix <PREFIX>, -statefile <STATEFILE>, -errors <i>, -threads <i>, -loglevel <LEVEL>, -instances <i>, -beagle_order <order> and -beagle_scaling <default|none|dynamic|always> are the ones that want a value handed to them. the rest are just vibes. ✨

🎀 EXAMPLES 🎀

here's how it actually looks when you run it, copy these exactly bestie:

beast2-mcmc test.xml
beast2-mcmc -window test.xml
beast2-mcmc -help

🫶 AUTHOR 🫶

this manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. thank you Andreas, we appreciate you 🥹💜

and that's the whole page, bestie!! we did it. 🎉 this was beast2-mcmc version 2.4.1, dated May 2016, and honestly it ate. go run your MCMC, you main character. 🦋✨💖

📦 where this page comes from