Command Reference for MrBayes ver. 3.1 (c) John P. Huelsenbeck and Fredrik Ronquist *************************************************************************** * * * 1. Command summary * * * *************************************************************************** --------------------------------------------------------------------------- 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 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"). --------------------------------------------------------------------------- *************************************************************************** * * * 2. MrBayes commands * * * *************************************************************************** --------------------------------------------------------------------------- About This command provides some general information about the program. --------------------------------------------------------------------------- --------------------------------------------------------------------------- Acknowledgments This command shows the authors' acknowledgments. --------------------------------------------------------------------------- --------------------------------------------------------------------------- Charset This command defines a character set. The format for the charset command is charset = For example, "charset first_pos = 1-720\3" defines a character set called "first_pos" that includes every third site from 1 to 720. The character set name cannot have any spaces in it. The slash (\) is a nifty way of telling the program to assign every third (or second, or fifth, or whatever) character to the character set. This option is best used not from the command line, but rather as a line in the mrbayes block of a file. Note that you can use "." to stand in for the last character (e.g., charset 1-.\3). --------------------------------------------------------------------------- --------------------------------------------------------------------------- Charstat This command shows the status of all the characters. The correct usage is charstat After typing "charstat", the character number, whether it is excluded or included, and the partition identity are shown. The output is paused every 100 characters. This pause can be turned off by setting autoclose to "yes" (set autoclose=yes). --------------------------------------------------------------------------- --------------------------------------------------------------------------- Citations This command shows a thorough list of citations you may consider using when publishing the results of a MrBayes analysis. --------------------------------------------------------------------------- --------------------------------------------------------------------------- Comparetree This command compares the trees in two files, called "filename1" and "filename2". It will output a bivariate plot of the split frequencies as well as plots of the tree distance as a function of the generation. The plots can be used to get a quick indication of whether two runs have con- verged onto the same set of trees. The "Comparetree" command will also produce a ".parts" file and a ".dists" file (these file endings are added to the end of the "Outputname"). The ".parts" file contains the paired split frequencies from the two tree samples; the ".dists" file contains the tree distance values. Note that the "Sumt" command provides a different set of convergence diagnostics tools that you may also want to explore. Un- like "Comparetree", "Sumt" can compare more than two tree samples and will calculate consensus trees and split frequencies from the pooled samples. Parameter Options Current Setting -------------------------------------------------------- Filename1 temp.t Filename2 temp.t Outputname temp.comp Burnin 0 --------------------------------------------------------------------------- --------------------------------------------------------------------------- Constraint This command defines a tree constraint. The format for the constraint command is constraint = A list of taxa can be specified using a taxset, taxon names, or taxon numbers. A probability must also be specified. For now, MrBayes ignores this probability value and treats the constraint as an absolute requirement of trees. That is, trees that are not compatible with the constraint have zero prior (and hence zero posterior) probability. Future releases of MrBayes will use the probability value to determine how much more probable a tree is that contains the constraint than a tree without the constraint. For example, the following command constraint example 100 = taxon_2 taxon_3 defines a constraint called "example" that includes two taxa. In future releases of MrBayes, trees that contain a clade with those two taxa together will have a prior probability that is 100 times that of trees without the constraint. In the current version, the probability value will be ignored and trees without the two taxa together will not be sampled. If you are interested in inferring ancestral states for a particular node, you need to constrain that node first using the 'constraint' command. For more information on how to infer ancestral states, see the help for the 'report' command. It is important to note that simply defining a constraint using this command is not sufficient for the program to actually implement the constraint in an analysis. You must also specify the constraints using 'prset topologypr = constraints ()'. For more infor- mation, see the help on the 'prset' command. --------------------------------------------------------------------------- --------------------------------------------------------------------------- Ctype This command sets the character ordering for standard-type data. The correct usage is: ctype : The available options for the specifier are: unordered -- Movement directly from one state to another is allowed in an instant of time. ordered -- Movement is only allowed between adjacent characters. For example, perhaps only between 0 <-> 1 and 1 <-> 2 for a three state character ordered as 0 - 1 - 2. irreversible -- Rates of change for losses are 0. The characters to which the ordering is applied is specified in manner that is identical to commands such as "include" or "exclude". For example, ctype unordered: 10 23 45 defines charactes 10, 23, and 45 to be of type ordered. Similarly, ctype irreversible: 54 - 67 71-92 defines characters 54 to 67 and characters 71 to 92 to be of type irreversible. You can use the "." to denote the last character, and "all" to denote all of the characters. Finally, you can use the specifier "\" to apply the ordering to every n-th character or you can use predefined charsets to specify the character. Only one ordering can be used on any specific application of ctype. If you want to apply different orderings to different characters, then you need to use ctype multiple times. For example, ctype ordered: 1-50 ctype irreversible: 51-100 sets characters 1 to 50 to be ordered and characters 51 to 100 to be irreversible. The ctype command is only sensible with morphological (here called "standard") characters. The program ignores attempts to apply char- acter orderings to other types of characters, such as DNA characters. --------------------------------------------------------------------------- --------------------------------------------------------------------------- Databreaks This command is used to specify breaks in your input data matrix. Your data may be a mixture of genes or a mixture of different types of data. Some of the models implemented by MrBayes account for nonindependence at adjacent characters. The autocorrelated gamma model, for example, allows rates at adjacent sites to be correlated. However, there is no way for such a model to tell whether two sites, adjacent in the matrix, are actually separated by many kilobases or megabases in the genome. The databreaks command allows you to specify such breaks. The correct usage is: databreaks ... For example, say you have a data matrix of 3204 characters that include nucleotide data from three genes. The first gene covers characters 1 to 970, the second gene covers characters 971 to 2567, and the third gene covers characters 2568 to 3204. Also, let's assume that the genes are not directly adjacent to one another in the genome, as might be likely if you have mitochondrial sequences. In this case, you can specify breaks between the genes using: databreaks 970 2567; The first break, between genes one and two, is after character 970 and the second break, between genes two and three, is after character 2567. --------------------------------------------------------------------------- --------------------------------------------------------------------------- Delete This command deletes taxa from the analysis. The correct usage is: delete ... A list of the taxon names or taxon numbers (labelled 1 to ntax in the order in the matrix) or taxset(s) can be used. For example, the following: delete 1 2 Homo_sapiens deletes taxa 1, 2, and the taxon labelled Homo_sapiens from the analysis. You can also use "all" to delete all of the taxa. For example, delete all deletes all of the taxa from the analysis. Of course, a phylogenetic anal- ysis that does not include any taxa is fairly uninteresting. --------------------------------------------------------------------------- --------------------------------------------------------------------------- Deroot This command deroots the user tree. If the tree is already unrooted, a warning is issued. The correct usage is "deroot". --------------------------------------------------------------------------- --------------------------------------------------------------------------- Disclaimer This command shows the disclaimer for the program. In short, the disclaimer states that the authors (John Huelsenbeck and Fredrik Ronquist) are not responsible for any silly things you may do to your computer or any unforseen but possibly nasty things the computer program may inadvertently do to you. --------------------------------------------------------------------------- --------------------------------------------------------------------------- Exclude This command excludes characters from the analysis. The correct usage is exclude or exclude - or exclude or some combination thereof. Moreover, you can use the specifier "\" to exclude every nth character. For example, the following exclude 1-100\3 would exclude every third character. As a specific example, exclude 2 3 10-14 22 excludes sites 2, 3, 10, 11, 12, 13, 14, and 22 from the analysis. Also, exclude all excludes all of the characters from the analysis. Excluding all characters does not leave you much information for inferring phylogeny. --------------------------------------------------------------------------- --------------------------------------------------------------------------- Execute This command executes a file called . The correct usage is: execute For example, execute replicase.nex would execute the file named "replicase.nex". This file must be in the same directory as the executable. --------------------------------------------------------------------------- --------------------------------------------------------------------------- Help This command provides useful information on the use of this program. The correct usage is help which gives a list of all available commands with a brief description of each or help which gives detailed information on the use of . --------------------------------------------------------------------------- --------------------------------------------------------------------------- Include This command includes characters that were previously excluded from the analysis. The correct usage is include or include - or include or some combination thereof. Moreover, you can use the specifier "\" to include every nth character. For example, the following include 1-100\3 would include every third character. As a specific example, include 2 3 10-14 22 includes sites 2, 3, 10, 11, 12, 13, 14, and 22 from the analysis. Also, include all includes all of the characters in the analysis. Including all of the characters (even if many of them are bad) is a very total-evidence-like thing to do. Doing this will make a certain group of people very happy. On the other hand, simply using this program would make those same people unhappy. --------------------------------------------------------------------------- --------------------------------------------------------------------------- Link This command links model parameters across partitions of the data. The correct usage is: link = ( or ) The list of parameters that can be linked includes: Tratio -- Transition/transversion rate ratio Revmat -- Substitution rates of GTR model Omega -- Nonsynonymous/synonymous rate ratio Statefreq -- Character state frequencies Shape -- Gamma shape parameter Pinvar -- Proportion of invariable sites Correlation -- Correlation parameter of autodiscrete gamma Switchrates -- Switching rates for covarion model Brlens -- Branch lengths of tree Topology -- Topology of tree Speciationrates -- Speciation rates for birth-death process Extinctionrates -- Extinction rates for birth-death process Theta -- Parameter for coalescence process Growthrate -- Growth rate of coalescence process For example, link shape=(all) links the gamma shape parameter across all partitions of the data. You can use "showmodel" to see the current linking status of the characters. For more information on this command, see the help menu for link's converse, unlink ("help unlink"); --------------------------------------------------------------------------- --------------------------------------------------------------------------- Log This command allows output to the screen to also be output to a file. The useage is: log start/stop filename= append/replace The options are: Start/Stop -- Starts or stops logging of output to file. Append/Replace -- Either append to or replace existing file. Filename -- Name of log file (currently, the name of the log file is "log.out"). --------------------------------------------------------------------------- --------------------------------------------------------------------------- Lset This command sets the parameters of the likelihood model. The likelihood function is the probability of observing the data conditional on the phylo- genetic model. In order to calculate the likelihood, you must assume a model of character change. This command lets you tailor the biological assumptions made in the phylogenetic model. The correct usage is lset =