---
name: "beast2-mcmc"
section: "1"
platform: "linux"
package: "beast2-mcmc"
version: "2.7.6+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/beast2-mcmc"
---

# beast2-mcmc(1)

Bayesian MCMC phylogenetic inference

## NAME

beast2-mcmc - Bayesian MCMC phylogenetic inference

## SYNOPSIS

**beast2-mcmc** \[-window\] \[-options\] \[-working\] \[-seed\] \[-prefix \<PREFIX\>\] \[-statefile \<STATEFILE\>\] \[-overwrite\] \[-resume\] \[-validate\] \[-errors \<i\>\] \[-threads \<i\>\] \[-java\] \[-noerr\] \[-loglevel \<LEVEL\>\] \[-instances \<i\>\] \[-beagle\] \[-beagle\_info\] \[-beagle\_order \<order\>\] \[-beagle\_CPU\] \[-beagle\_GPU\] \[-beagle\_SSE\] \[-beagle\_single\] \[-beagle\_double\] \[-beagle\_scaling \<default\|none\|dynamic\|always\>\] \[-help\] \[-version\] \[\<input-file-name\>\]

## DESCRIPTION

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also 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. Included is a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

This is no new upstream version of beast-mcmc (1.x) but rather a rewritten version.

## OPTIONS

**-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

## EXAMPLES

-

  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.