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# Global variables:
DATA = LSU
METHOD = bionj
# Sequences:
# The alphabet to use:
# DNA, RNA or Protein
alphabet=DNA
# The sequence file to use (sequences must be aligned!)
input.sequence.file=../Data/$(DATA).phy
# The alignment format:
input.sequence.format=Phylip(order=sequential, type=extended)
#Sites to use:
# all, nogap or complete (=only resolved chars)
input.sequence.sites_to_use = complete
# Specify a maximum amount of gaps: may be an absolute number or a percentage.
input.sequence.max_gap_allowed=100%
# Output the distance matrix if any.
output.matrix.file = $(DATA).mat
# ----------------------------------------------------------------------------------------
# Model specification
# ----------------------------------------------------------------------------------------
# See the manual for a description of the syntax and available options.
#
model = HKY85(kappa=2.843, theta=0.5, theta1=0.5, theta2=0.5, useObservedFrequencies=yes)
rate_distribution = Gamma(n=4, alpha=0.358)
# Tree reconstruction method [wpgma|upgma|nj|bionj]
method = $(METHOD)
// Parameter estimation:
// - init = keep as initial values,
// - pairwise = estimate separately for each pair of sequences,
// - iterations = use iterations and ML to estimate these parameters globally.
optimization.method = init
optimization.verbose = 1
optimization.ignore_parameter =
optimization.max_number_f_eval = 10000
optimization.tolerance = 0.000001
optimization.message_handler = $(DATA).messages
optimization.profiler = $(DATA).profile
# Should we write the resulting tree? none or file name.
output.tree.file = $(DATA).$(METHOD).dnd
output.tree.format = Newick
# Bootstrap:
bootstrap.number = 10
bootstrap.approximate = no
# Set this to yes for detailed output when bootstrapping.
bootstrap.verbose = no
bootstrap.output.file = $(DATA).$(METHOD)_bstrees.dnd
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