---
name: "beast-mcmc"
section: "1"
platform: "linux"
package: "beast-mcmc"
version: "1.10.4+dfsg-7"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/beast-mcmc"
---

# beast-mcmc(1)

Bayesian evolutionary analysis sampling trees

## NAME

beast-mcmc - Bayesian evolutionary analysis sampling trees

## SYNOPSIS

**beast-mcmc** \[**OPTIONS**\] \[*input.xml*\]

**beast-mcmc** \[**-verbose** \| **-strict** \| **-window** \| **-options** \| **-working** \| **-seed** \| **-errors i** \| **-threads i** \| **-java** \| **-beagle** \| **-beagle\_info** \| **-beagle\_resource\_order** \| **-help** \| **input.xml**\]

## DESCRIPTION

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It is intended both as a method of reconstructing phylogenies and as a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suite of programs for analysing the results. There are three main areas of research for which the BEAUti/BEAST package is particularly applicable. These areas are species phylogenies for molecular dating, coalescent-based population genetics and measurably evolving populations (ancient DNA or time-stamped viral sequence data sets).

## OPTIONS

- **-verbose**

  verbose XML parsing messages

- **-strict**

  fail on non conforming BEAST XML file

- **-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

- **-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

## BUGS

The BEAST bug tracking system can be found at *https://github.com/beast-dev/beast-mcmc/issues*.

## SEE ALSO

[**beauti**(1)](/beauti/1.md).

## REFERENCES

• 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.

## AUTHORS

**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.