BAMBE

Bayesian Analysis in Molecular Biology and Evolution

Version 1.01 beta, October 1998

© Copyright 1998, Donald Simon & Bret Larget, Department of Mathematics and Computer Science, Duquesne University.


Run control file format

The run control file contains all of the run characteristics and tree and parameter initialization information. Here is a small example file.


#################### BAMBE Run Control File #################### 
# Last updated July 26, 1998   Change parameters as
# necessary.   Any text on a line after the symbol `#' is a
# comment. 

#
# run characteristics
#
seed=95730489               # 1 < odd integer < 2147483647 (2^31 - 1)
burn=5000                   # number of cycles to run burn algorithm 
burn-algorithm=global       # global or local
main-algorithm=local        # global or local
cycles=10000                # number of cycles to run main algorithm 
sample-interval=10          # interval to save information to file 
tune-interval=200           # interval to adapt tuning paramters during burn-in 
window-interval=200         # interval to print information to the screen 
tree-file=random            # random or name of file 
max-initial-tree-height=.2  # height of initial random tree
file-root=wrun1             # root name for output files
#
# model specification
#
parameter-update-interval=1 # number of tree updates after each paramter update 
                            # use 0 for no paramter updating 
update-kappa=true           # transition/tranversion parameters 
update-theta=true           # rate parameters 
update-pi=false             # use empirical relative frequencies, don't update 
molecular-clock=false       # true or false 
likelihood-model=HKY85      # F84, HKY85, TN93 are current choices 
category-list = (1,2,3)*    # Category pattern is 1,2,3,1,2,3,... 
                            # This is a codon position specific model. 
single-kappa=false          # Use separate kappa values for all site categories 
initial-kappa=4.0,3.3,6.19  # comma separated list 
                            # with equal to number of categories 
initial-theta=0.3,0.1,2.6   # warning in weighted average is not 1 
# 
# tuning parameters 
# 
initial-delta=0.2            
initial-kappa-delta=0.2 
theta-const=2000.0 
pi-const=2000.0 
#
# data file information
#
data-file=whales.dna        # file name
outgroup=31                 # position of outgroup species in data file 

In addition to this example, the distribution contains several other sample run control files.

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. Run parameters will be processed in the order we list them below. All options have default values, which are boldface in the following table.

Run control file options.
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 inference.
burn-algorithm global, local Algorithm to run during burn.
main-algorithm global and local Algorithm to run during production cycles.
cycles Any nonnegative integer.
Default is 6000
Number of cycles to run the main algorithm.
sample-interval Any positive integer.
Default is 200
During burn and main algorithms, the tree topology, log likelihoods, and parameters are written to files at each cycle divisible by this value.
parameter-update-interval Any nonnegative integer.
Default is 0
During the main algorithm, any "on" parameters are updated at each cycle divisible by this value.
update-kappa true or false Indicates if kappa parameter value(s) are updated.
update-theta true or false Indicates if theta parameter value(s) are updated.
update-pi true or false Indicates if pi parameter values are updated.
theta-const 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.
pi-const 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.
tune-interval 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, delta is halved.
window-interval Any nonnegative integer.
Default is 200
Interval at which tree topology and parameter values are printed to screen.
molecular-clock true or false Indicates if molecular clock is used during run of the main algorithm.
likelihood-model HKY85, F84, or TN93 Hasegawa, Kishino, Yano (1985),
Felsenstein's PHYLIP (1984),
Tamura-Nei (1993).
See section on likelihood models for more detail.
category-list A valid category list.
Default is 1*
A comma-separated list of categories with optional repeat counts and optionally one repetitive asterisk.
See the section on category lists for more details.
single-kappa 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.
initial-kappa Comma separated list of positive kappa values.
Default is 2.0,2.0,2.0 which assumes three rate categories.
If single-kappa is true, a warning is given if more than one value is specified. The first value will be used. If single-kappa is false, a value must be specified for each category in use.
initial-theta Comma separated list of positive theta values.
Default is 1.0,1.0,1.0 which assumes three rate categories.
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.
initial-ttp Comma separated list of positive transition/transversion parameter values.
Default is 1.0,1.0,1.0 which assumes three rate categories.
This is used only with TN93. There must be a value specified for each site-category used if TN93 is the chosen model.
initial-gamma Comma separated list of positive gamma values.
Default is 1.0,1.0,1.0 which assumes three rate categories.
This is used only with TN93. There must be a value specified for each site-category used if TN93 is the chosen model.
data-file 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.
initial-delta Positive number.
Default is 0.01
This tuning parameter is only used with the global algorithm. The smaller its value, the greater the tree acceptance rate will be.
initial-kappa-delta Positive number.
Default is 0.5
This tuning parameter is only used when the parameter-update-interval is positive and update-kappa is true. The smaller its value, the greater the parameter acceptance rate will be.
max-initial-tree-height Positive number.
Default is 0.1
This parameter is only used to generate an initial random tree.
tree-file Filename in directory program is run that contains initial tree in either BAMBE or Newick format, or random. If the value is random, the program generates a random tree from a flat distribution where each labeled history is equally likely. If the tree file is in Newick format, it needs to be specified by newick-format.
newick-format true or false. Indicates the format of the tree to read (if not random) and the format of the tree to print after the run.


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This page was most recently updated on October 19, 1998.

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