The online help was generated by Jeff Bates, Smithsonian Institution. jbates@lab.si.edu.
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").