The online help was generated by Jeff Bates, Smithsonian Institution.

Commands that are available from the command line or from a MrBayes block include:

About -- Describes the program
Acknowledgments -- Shows program acknowledgments
Charset -- Assigns a group of sites to a set
Charstat -- Shows status of characters
Citations -- Appropriate citation of program
Comparetree -- Compares the trees from two tree files
Constraint -- Defines a constraint on tree topology
Ctype -- Assigns ordering for the characters
Databreaks -- Defines nucleotide pairs (doublets) for stem models
Delete -- Deletes taxa from the analysis
Deroot -- Deroots user tree
Disclaimer -- Describes program disclaimer
Exclude -- Excludes sites from the analysis
Execute -- Executes a file
Help -- Provides detailed description of commands
Include -- Includes sites
Link -- Links parameters across character partitions
Log -- Logs screen output to a file
Lset -- Sets the parameters of the likelihood model
Manual -- Prints a command reference to a text file
Mcmc -- Starts Markov chain Monte Carlo analysis
Mcmcp -- Sets the parameters of a chain (without starting analysis)
Outgroup -- Changes outgroup taxon
Pairs -- Defines nucleotide pairs (doublets) for stem models
Partition -- Assigns a character partition
Plot -- Plots parameters from MCMC analysis
Prset -- Sets the priors for the parameters
Props -- Set proposal probabilities
Quit -- Quits the program
Reassemble -- Reassembles MPI output files
Report -- Controls how certain model parameters are reported
Restore -- Restores taxa
Root -- Roots user tree
Set -- Sets run conditions and defines active data partition
Showmatrix -- Shows current character matrix
Showmodel -- Shows model settings
Showtree -- Shows user tree
Sump -- Summarizes parameters from MCMC analysis
Sumt -- Summarizes trees from MCMC analysis
Taxastat -- Shows status of taxa
Taxset -- Assigns a group of taxa to a set
Unlink -- Unlinks parameters across character partitions
Usertree -- Defines a single user tree
Version -- Shows program version

Commands that should be in a NEXUS file (data block or trees block) include:

Begin -- Denotes beginning of block in file
Dimensions -- Defines size of character matrix
End -- Denotes end of a block in file
Endblock -- Alternative way of denoting end of a block
Format -- Defines character format in data block
Matrix -- Defines matrix of characters in data block
Translate -- Defines alternative names for taxa
Tree -- Defines a tree from MCMC analysis

Note that this program supports the use of the shortest unambiguous spelling of the above commands (e.g., "exe" instead of "execute").

Return to the main help page.

Return to the MrBayes home page.