© Copyright 2000, 2001, Donald Simon & Bret Larget, Department of Mathematics and Computer Science, Duquesne University.
#################### BAMBE Default Run Control File #################### # Last updated September 16, 1999 Change parameters as necessary. # Any text on a line after the symbol `#' is a comment. ######################################################################## # # general run settings # seed = 194024933 # 1 < odd integer < 2147483647 (2^31  1) burn = 1000 # number of cycles to run burn algorithm cycles = 6000 # number of cycles to run main algorithm burnalgorithm = global # global or local mainalgorithm = local # global or local usebeta = false # use scaled beta distribution modification of local windowinterval = 200 # interval to print information to the screen # # output run settings # sampleinterval = 10 # interval to save information to file fileroot = run1 # root name for output files newickformat = true # format of output tree, false implies bambe format # # model specification # molecularclock = true # true or false likelihoodmodel = HKY85 # F84, HKY85, TN93 are current choices categorylist = 1* # one site category singlekappa = false # use separate kappa values for all site categories initialkappa = 2.0 initialtheta = 1.0 estimatepi = true # use empirical relative frequencies #initialpia = 0.25 #initialpig = 0.25 #initialpic = 0.25 #initialpit = 0.25 #initialttp = 1.0 #initialgamma = 1.0 # # parameter updating # parameterupdateinterval = 1 # number of tree updates after each parameter update # use 0 for no parameter updating updatekappa = true # transition/tranversion bias parameters, not used with TN93 updatetheta = true # substitution rate parameters updatepi = true # base relative frequency parameters updatettp = true # transition/transversion parameters for TN93 updategamma = true # transition/transversion parameters for TN93 # # tuning parameters # tuneinterval = 200 # interval to adapt globaltune during burnin globaltune = 0.01 # half window width for global localtune = 0.19 # stretch parameter for local thetatune = 2000.0 # Dirichlet parameter for theta update pitune = 2000.0 # Dirichlet parameter for pi update kappatune = 0.1 # half window width for kappa update #ttptune = 0.1 # half window width for ttp update #gammatune = 0.1 # half window width for gamma update betatune = 10.0 # Beta parameter for local update (with beta) # # data file # datafile = infile # file name outgroup = 1 # # initial tree information # initialtreetype = random # random, upgma, neighborjoining, newick, or bambe maxinitialtreeheight = 0.1 # height of initial random tree #treefile = treefile # name of file with initial tree (newick or bambe)
All options may be entered into the run control file in any order. The symbol `=' appears after the name of the option followed by the value. White space may separate the run parameter name, the equal sign, and the value. Any text after the symbol `#' on a line is a comment and ignored. All options have default values, which are boldface in the following table.
Option  Choices  Description 

seed 
1 < odd integer < 2147483647. Default is 194024933 
Seed for random number generator. 
burn 
Any nonnegative integer. Default is 1000 
Number of cycles to run the burn algorithm. Parameter values are not updated during burn. User should discard these cycles and the initial cycles of the main algorithm before summarizing the remaining results. 
cycles 
Any nonnegative integer. Default is 6000 
Number of cycles to run the main algorithm. 
burnalgorithm 
global or local  Algorithm to run during burn. 
mainalgorithm 
global or local  Algorithm to run during production cycles. 
usebeta
 true or false  Indicates whether or not to use the Beta distribution modification of the local algorithm. 
windowinterval 
Any nonnegative integer. Default is 200 
Interval at which tree topology and parameter values are printed to screen. 
sampleinterval 
Any positive integer. Default is 10 
During burn and main algorithms, the tree topology, log likelihoods, and parameters are written to files at each cycle divisible by this value. 
fileroot
 Any valid file name. Default is run1  Output files use fileroot in their file names. 
newickformat 
true or false.  Indicates the format of the output tree. False implies BAMBE format which mimics the internal data structure of the tree and is useful for debugging. 
molecularclock 
true or false  Indicates if molecular clock is used during run of the main algorithm. 
likelihoodmodel 
HKY85, F84, or TN93  Hasegawa, Kishino, Yano (1985), Felsenstein's PHYLIP (1984), TamuraNei (1993). See section on likelihood models for more detail. 
categorylist 
A valid category list. Default is 1* A commaseparated list of categories with optional repeat counts and optionally one repetitive asterisk.  See the section on category lists for more details. 
singlekappa 
true or false  If true, the same kappa parameter is used for all site categories. If false, there are different values for different site categories. It has no effect if there is only one rate category. 
initialkappa 
Comma separated list of positive kappa values. Default is 2.0  If singlekappa is true, a warning is given if more than one value is specified. The first value will be used. If singlekappa is false, a value must be specified for each category in use. 
initialtheta 
Comma separated list of positive theta values. Default is 1.0  The weighted average of these values should be 1, with weights given by the proportion of sites in each site category. (Renormalization is automatic and a warning given if the condition fails.) If there are an equal number of sites in each category, for example, the numbers should average to 1. 
estimatepi
 true or false  If true, the initial stationary probabilities for each base in each category are estimated by the relative frequencies with which they appear in the data. 
initialpia
 Comma separated list of positive numbers between 0 and 1. Default is 0.25 if estimatepi is false.
 The initial stationary probability of the base A.
There must be a value specified for each sitecategory used
if estimatepi is false. 
initialpig
 Comma separated list of positive numbers between 0 and 1. Default is 0.25 if estimatepi is false.
 The initial stationary probability of the base G.
There must be a value specified for each sitecategory used
if estimatepi is false. 
initialpic
 Comma separated list of positive numbers between 0 and 1. Default is 0.25 if estimatepi is false.
 The initial stationary probability of the base C.
There must be a value specified for each sitecategory used
if estimatepi is false. 
initialpit
 Comma separated list of positive numbers between 0 and 1. Default is 0.25 if estimatepi is false.
 The initial stationary probability of the base T.
There must be a value specified for each sitecategory used
if estimatepi is false. 
initialttp 
Comma separated list of positive transition/transversion parameter values. Default is 1.0  This is used only with TN93. There must be a value specified for each sitecategory used if TN93 is the chosen model. 
initialgamma 
Comma separated list of positive gamma values. Default is 1.0  This is used only with TN93. There must be a value specified for each sitecategory used if TN93 is the chosen model. 
parameterupdateinterval 
Any nonnegative integer. Default is 1 
During the main algorithm, any ``on'' parameters are updated at each cycle divisible by this value. 
updatekappa 
true or false  Indicates if kappa parameter value(s) are updated. Not used in model TN93. 
updatetheta 
true or false  Indicates if theta parameter value(s) are updated. 
updatepi 
true or false  Indicates if pi parameter values are updated. 
updatettp 
true or false  Indicates if the ttp parameter values are updated. Only used if the model is TN93. 
updategamma 
true or false  Indicates if the gamma parameter values are updated. Only used if the model is TN93. 
tuneinterval 
Any positive integer. Default is 200 
While running global during the burn, if the acceptance rate for tree proposal falls below 15% during this interval, globaltune is halved. 
globaltune 
Positive number. Default is 0.01 
This tuning parameter is only used with the global algorithm during burn. The smaller its value, the greater the tree acceptance rate will be. 
localtune 
Positive number. Default is 0.19 
This tuning parameter is only used with the local algorithm. It modulates the size of a maximal stretch. The smaller its value, the greater the tree acceptance rate will be. 
thetatune 
Any positive real number Default is 2000.0 
Tuning parameter used during update of theta value(s). The larger its value, the more likely proposals are to be accepted. 
pitune 
Any positive real number Default is 2000.0 
Tuning parameter used during update of pi values. The larger its value, the more likely proposals are to be accepted. 
kappatune 
Positive number. Default is 0.1 
This tuning parameter is only used when
parameterupdateinterval is positive
and updatekappa is true.
The smaller its value, the greater the parameter acceptance rate will be. 
ttptune 
Positive number. Default is 0.1 
This tuning parameter is only used when
parameterupdateinterval is positive
and updatettp is true.
The smaller its value, the greater the parameter acceptance rate will be. 
gammatune 
Positive number. Default is 0.1 
This tuning parameter is only used when
parameterupdateinterval is positive
and updategamma is true.
The smaller its value, the greater the parameter acceptance rate will be. 
betatune 
Positive number. Default is 10.0 
This tuning parameter is only used if
usebeta is true
The larger its value, the greater the parameter acceptance rate will be. 
datafile 
Filename in directory program is run that contains data Default is infile 
Data may be in either BAMBE or CLUSTAL formats. The format is automatically recognized. 
outgroup 
Positive integer with outgroup in order of data file. Default is 1 
This is ignored if a molecular clock is assumed. In the absence of a clock, trees and tree topologies are printed with the outgroup emerging directly from the root. 
initialtreetype 
random, upgma, neighborjoining, newick, or bambe  random selects a tree from the prior; upgma sets the initial (clock) tree to the UPGMA tree using maximum likelihood distances with the specified model and initial parameter values; neighborjoining sets the initial (nonclock) tree to the neighbor joining tree using maximum likelihood distances with the specified model and initial parameter values; newick reads in an initial tree in Newick format from a file; bambe reads in an initial tree in BAMBE format from a file. 
maxinitialtreeheight 
Positive number. Default is 0.1 
This parameter is only used to generate an initial random tree. 
treefile 
Filename in directory in which the program is run
that contains the initial tree. Default is treefile.  This is only used if initialtreetype
is newick or bambe, and the format should match.

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