[commandline]
aligned = False
auto = False
datatype = dna
input = .
job = satejob
keepalignmenttemps = True
keeptemp = True
multilocus = True
raxml_search_after = False
temporaries = sateout
timesfile = time.txt
treefile = starting.tre
two_phase = False
untrusted = False

[sate]
after_blind_iter_term_limit = -1
after_blind_iter_without_imp_limit = 1
after_blind_time_term_limit = -1.0
after_blind_time_without_imp_limit = -1.0
aligner = mafft
blind_after_iter_without_imp = -1
blind_after_time_without_imp = -1.0
blind_after_total_iter = -1
blind_after_total_time = -1.0
blind_mode_is_final = True
break_strategy = longest
iter_limit = -1
iter_without_imp_limit = -1
max_mem_mb = 2048
max_subproblem_frac = 0.5
max_subproblem_size = 82
merger = muscle
move_to_blind_on_worse_score = True
num_cpus = 1
output_directory = sateout
return_final_tree_and_alignment = False
start_tree_search_from_current = True
time_limit = -1.0
time_without_imp_limit = -1.0
tree_estimator = fasttree

