#################### 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 = 100000                   # number of cycles to run burn algorithm 
cycles = 100000                 # number of cycles to run main algorithm 
burn-algorithm = global       # global or local
main-algorithm = local        # global or local
use-beta = false              # use scaled beta distribution modification of local
window-interval = 5000         # interval to print information to the screen 

#
# output run settings
#
sample-interval = 200         # interval to save information to file
file-root = run1              # root name for output files
newick-format = true          # format of output tree, false implies bambe format

#
# model specification
#
molecular-clock = false        # true or false 
likelihood-model = HKY85      # F84, HKY85, TN93 are current choices 
category-list = 1*            # one site category
single-kappa = true          # use separate kappa values for all site categories 
initial-kappa = 2.0
initial-theta = 1.0
estimate-pi = true            # use empirical relative frequencies
#initial-pia = 0.25
#initial-pig = 0.25
#initial-pic = 0.25
#initial-pit = 0.25
#initial-ttp = 1.0
#initial-gamma = 1.0

#
# parameter updating
#
parameter-update-interval = 1 # number of tree updates after each parameter update 
                              # use 0 for no parameter updating 
update-kappa = true           # transition/tranversion bias parameters, not used with TN93
update-theta = true           # substitution rate parameters 
update-pi = true              # base relative frequency parameters
update-ttp = true             # transition/transversion parameters for TN93
update-gamma = true           # transition/transversion parameters for TN93

# 
# tuning parameters
# 
tune-interval = 50         # interval to adapt global-tune during burn-in 
global-tune = 0.01          # half window width for global
local-tune = 0.19           # stretch parameter for local
theta-tune = 2000.0         # Dirichlet parameter for theta update
pi-tune = 2000.0            # Dirichlet parameter for pi update
kappa-tune = 0.1            # half window width for kappa update
#ttp-tune = 0.1              # half window width for ttp update
#gamma-tune = 0.1            # half window width for gamma update
beta-tune = 10.0            # Beta parameter for local update (with beta)

#
# data file
#
data-file = dna.in          # file name
outgroup = 1

#
# initial tree information
#
initial-tree-type = neighbor-joining    # random, upgma, neighbor-joining, newick, or bambe  
max-initial-tree-height = 0.1 # height of initial random tree
#tree-file = treefile          # name of file with initial tree (newick or bambe)