BEAST-MCMC(1)

💅 NAME 💅

okay so bestie, this is beast-mcmc(1) from the BEAST-MCMC Manual, and it's literally just: Bayesian evolutionary analysis sampling trees. that's the whole vibe. 🦋

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✨ SYNOPSIS ✨

like, here's how you actually call her:

beast-mcmc [OPTIONS] [input.xml]

and here's the long-form version, no cap:

beast-mcmc [-verbose | -strict | -window | -options | -working | -seed |
           -errors i | -threads i | -java | -beagle | -beagle_info |
           -beagle_resource_order | -help | input.xml]

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🌸 DESCRIPTION 🌸

okay so BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. periodt. she's orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. 👑

the way she's intended BOTH as a method of reconstructing phylogenies AND as a framework for testing evolutionary hypotheses without conditioning on a single tree topology... we love a multi-hyphenate. 💖

and here's the iconic part: BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. slay.

she also comes with a simple to use user-interface program for setting up standard analyses, plus a whole suite of programs for analysing the results. a whole girlband. 🎀

there are three main areas of research for which the BEAUti/BEAST package is particularly applicable, and they are:

1. species phylogenies for molecular dating
2. coalescent-based population genetics
3. measurably evolving populations (ancient DNA or time-stamped viral sequence data sets)

like, the range?? immaculate. ✨

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💅 OPTIONS 💅

one bullet per flag bestie, i'm not skipping a single one:

• -verbose — verbose XML parsing messages. she's gonna talk. a lot. 🗣️
• -strict — fail on non conforming BEAST XML file. no sloppy XML in this house. 🙅
• -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 🎲 (reproducibility queen)
• -errors i — maximum number of numerical errors before stopping 🛑
• -threads i — the number of computational threads to use (default 1) 🧵
• -java — use Java only, no native implementations ☕
• -beagle — use beagle library if available 🐶
• -beagle_info — show information on available beagle resources 📋
• -beagle_resource_order — set order of beagle resources 🔢
• -help — print usage screen 🆘

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💀 BUGS 💀

found a bug? not me. 😭 the BEAST bug tracking system can be found at https://github.com/beast-dev/beast-mcmc/issues.

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🫶 SEE ALSO 🫶

beauti(1). that's her sister. iykyk. 💜

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📚 REFERENCES 📚

the receipts, in order:

• Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology 7:214.
• Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88.
• Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185-1192.
• Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307-1320.

academic baddies fr fr. 🔥

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👑 AUTHORS 👑

the main characters responsible for all of this:

• Alexei J. Drummond — Copyright holder for BEAST.
• Andrew Rambaut — Copyright holder for BEAST.
• Marc A. Suchard — Copyright holder for BEAST.
• Felix Feyertag <felix.feyertag@googlemail.com> — Prepared this manpage in DocBook XML for the Debian distribution.

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and that's the whole page bestie! this one's living in BEAST 1.5.3, dated 05/28/2010 — vintage, retro, still eating. 💖✨🎀