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# Global variables:
DATA = LSU
# Sequences:
# The laphabet to use:
# DNA, RNA or Protein
alphabet=DNA
use.gaps=no
# The sequence file to use (sequences must be aligned!)
input.sequence.file=../Data/$(DATA).phy
# The alignment format:
input.sequence.format=Phylip(order=sequential, type=extended)
#Sites to use:
# all, nogap or complete (=only resolved chars)
input.sequence.sites_to_use = complete
# Specify a maximum amount of gaps: may be an absolute number or a percentage.
input.sequence.max_gap_allowed = 100%
input.tree.file = ../Data/$(DATA).dnd
input.tree.format = Newick
optimization.topology = yes
# Should we write the resulting tree? none or file name.
output.tree.file = $(DATA).pars.dnd
output.tree.format = Newick
# Bootstrap:
bootstrap.number = 1000
bootstrap.output.file = $(DATA).pars_bstrees.dnd
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