DPPDIV

command line this example:

dppdiv-pthreads -T 16 -in infile.txt -tre tree.tre  (required)

-n 1000000  -pf 100 -sf 100  -out test1.32  -pm 3.0  -ra 2.0 -rb 4.0  -bdr 2.3 -s1 12345 -s2 12345  -hsc 1.2  -hsh 2.0 
 
upload_calfile_ is an optional Upload node calibrations file (optional)   
 
-n 1000000 -pf 100 -sf 100 -out test         -pm 3.0 -ra 2.0 -rb 4.0 -s1 757 -s2 945667 -hsh 2.0 

this test passes

this run is produced by this set of instructions:


dpm_hyperprior_=0  (switch 0/1 default=0) requires uploaded cal file
gamma_hyperpriorshape_=2.0  float Shape for gamma hyper prior on alpha concentration parameter(-hsh
gamma_hyperpriorscale_= float Scale for gamma hyper prior on alpha concentration parameter (-hsc
gamma_omrates_=4.0 float Scale for gamma om rates (-rb) vder=4.0
gamma_shape_=2.0 float Shape for gamma on rates (-ra)
hyperprior_oncal_=0 switch 0/1 (Hyperprior on calibrations from a gamma- (-ghp) ndefault = 0 requires uploaded cal file
input_branchlengths_=0  switch 0/1 Use input branch lengths (-ubl) default = 0
mcmc_cycles_=1000000 integer default 1,000,000
npr_value_=3 excl, 1,2,3,4 allowed values, 	1=Uniform;2=Yule;3=cbd,4=cbd fix
offset_exponential_=0 switch 0/1 (All calibrated nodes are offset exponential (-exhp) default=0) requires uploaded cal file
outfile_prefix_=fun  string Output file prefix
print_freq_=100  integer Print frequency default=100
print_moves_=0 >Print moves to .info.out file (-vb) default=0
prior_mean_=3.0 float Prior mean of number of rate categories (-pme_ext_= float (Relative Extinction Rate (-bda ))default is null
ro_nodemove_=0 switch 0/1 Use random-order node moves (-rdn)dfault0
run_uncorrelated_=0   Run under uncorrelated gamma-distributed rates (-urg) default 0
runtime_=0.25 float default =0.25
sample_frequency_=100 integer Sample frequency default 100
starting_val_diverserate_= float starting_val_diverserate default is null
seed1_=12345 integer
seed2_=12345 integer 
single_nodemove_=0 switch 0/1 Use single node move (-snm)
soft_bounds_=0 switch 0/1 (Turn on soft bounds on calibrated nodes (-soft default 0) requires uploaded cal file
strict_clock_=0 Run under strict clock (and estimate substitution rate) (-clok default 0)
turnoff_move_=0 excl, 1,2,3,4,5,6 Turn off this move