CLEARCUT
runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly)
infile_ - Primary Input File
alignment_or_ - Switch - My data is an alignment (no =distance matrix)
datatype_is_ - Excl - Datatype:
corr_model_ - Excl - Correction Model for Computing Distance Matrix
Section: ****************************************************************************
adv_opts
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use_trad_ - Switch - Use traditional Neighbor-Joining algorithm. (-N)
shuff_matrix_ - Switch - Randomly shuffle the distance matrix. (-S)
join_det_ - Switch - Attempt joins deterministically. (-r)
spec_seed_ - Switch - Explicitly set the PRNG seed to a specific value. (-s)
seed_val_ - Integer -
Section: ****************************************************************************
output_opts
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matrix_out_ - Switch - Output a Distance Matrix
ntrees_out_ - Integer - Number of trees to write out
exp_dist_ - Switch - Exponential notation in distance output (-E)
exp_brl_ - Switch - Exponential notation for branch lengths (-e)
tree_results_ - Results -
matrix_results_ - Results -
commandline_ - Results -
job_info_ - Results -