Run Options

There are a number of simple and more complex options to run datasets through treePL. These should be placed in the configuration file that would be run like

treePL configuration

This list is in the format

optionname [description]

or

optionname = someparameter [description]

On to the list of options

treefile = filename [the name of the file with the newick tree to transform]
smooth = number [the smoothing value]
numsites = integer [the number of sites in the alignment that created the tree]
mrca = mrcaname mrcataxa1 mrcataxa2 [MRCA that will be used for calibrations]
min = mrcaname date [minimum calibration with mrca name and date]
max = mrcaname date [maximum calibration with mrca name and date]
outfile = filename [the file that the transformed tree will be written to]
thorough [designate that you want a thorough analysis]
prime [designate that you want to determine the best optimization parameters]
opt = integer [set the gradient based optimizer]
optad = integer [set the autodiff based optimizer]
optcvad = integer [set the autodiff cross validation based optimizer]
cv [designate that you want to do a cross validation analysis]
randomcv [designate that you want to do random sampled cross validation]
cvoutfile = filename [designate where you want the cross validation results to be printed, default = cv.out]
cvstart = number [set where you want to start cross validation, default = 1000]
cvstop = number [set where you want to stop cross validation, default = 0.1]
nthreads = integer [number of threads]
cviter = number [the number of cross validation total optimization iterations, default = 2]
pliter = number [the number of penalized likelihood total optimization iterations, default = 2]
cvsimaniter = number [the number of cross validation simulated annealing iterations, default = 5000]
plsimaniter = number [the number of penalized likelihood simulated annealing iterations, default = 5000]
log_pen [rate penalty will use log instead of additive function]
seed = number [seed for random number generator, default = clock]