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