PARALLELSTRUCTURE_XSEDE


infile_ = 	will be named data.txt	
joblist_file_ = will be named joblist.txt required
					
runtime_ = (Float, default=0.5) Maximum Hours to Run (up to 168 hours)
set_numinds_ = (Integer, no default) Number of individuals in the population (NUMINDS) required value
set_numloci_ = (Integer, no default) Number of loci in the dataset (NUMLOCI) required value
set_ploidy_ = (Integer, no default) Ploidy of the dataset (PLOIDY) required value
set_missing_ = (Integer, no default) Value given to missing genotype data (MISSING) required value
set_onerowperind_ = (Switch, default=0) The data for each individual are arranged in a single row (ONEROWPERIND)
set_labels_ =  (Switch, default=0) Input file contains labels (names) for each individual (LABEL)
use_popinfo_ = (Switch, default=0) Use prior population information to assign individuals to clusters (USEPOPINFO)
set_popdata_ = (Switch, default=0) Input file contains a user-defined population-of-origin for each individual (POPDATA)
set_popflag_ = (Switch, default=0) Input file contains an indicator variable which says whether to use popinfo (POPFLAG) only when use_popinfo=1.
set_locdata_ = (Switch, default=0) Input file contains a user-defined sampling location for each individual (LOCDATA) only when use_locprior=1
set_phenotype_ =  (Switch, default=0) Input file contains a column of phenotype information (PHENOTYPE)
set_markernames_ = (Switch, default=0) The top row of the data file contains a list of L names corresponding to the markers  used (MARKERNAMES)	
set_recessivealleles_ = (Switch, default=0) Next row of data file contains a list of L integers indicating which alleles are recessive at each locus (RECESSIVEALLELES)
use_linkagemodel_ = (Switch, default=0)	Use the linkage model (LINKAGE)				
set_phased_ = (Switch, default=0)  Indicates that data are in correct phase (PHASED), use_linkagemodel=1
set_phaseinfo_ = (Switch, default=0) The row(s) of genotype data for each individual are followed by a row of information about haplotype phase (PHASEINFO), when use_linkagemodel=1 & set_phased = 0	
set_noadmix_ = (Switch, default=0) Assume the model without admixture (NOADMIX)
use_locprior_ = (Switch, default=0) Use location information to improve the performance on data that are weakly informative about structure (LOCPRIOR)
use_inferalpha_ = (Switch, default=0) Infer the value of the model parameter alpha from the data (INFERALPHA), only when set_noadmix=0			
use_popalphas_ = (Switch, default=0) Infer a separate alpha for each population (POPALPHAS)
set_alpha_ = (float, no default) Dirichlet parameter for degree of admixture (ALPHA)	
use_freqscorr_ = (Float, no default) Use the F model, in which the allele frequencies are correlated across populations (FREQSCORR)
set_fpriormean_ = (Float, no default) Set mean FPRIORMEAN for Fk (FPRIORMEAN)
set_fpriorsd_ = (Float, no default) Set std deviation for Fk (FPRIORSD)
use_onefst_= (Switch, default=0) Assume the same value of Fk for all populations (ONEFST)
set_gensback_= (integer, no default) Set  value for G (GENSBACK). Only when use_popinfo=1)
set_migrprior_ = (Float, no default) Set migration prior (MIGRPRIOR) Sensible values might be in the range 0.001—0.1.
use_pfrompopflagonly_ = (Switch, default=0) Update the allele frequencies, P , using only a prespecified subset of the individuals (PFROMPOPFLAGONLY), only when set_popflag=1
use_locispop_ = (Switch, default=0) Use the PopData Column for Location data (LOCISPOP)
set_locpriorinit_= (float, default=1) Initial value for the LOCPRIOR parameter r (LOCPRIORINIT)
set_maxlocprior_= (Integer, default=20)	MAXLOCPRIOR (double) Range of r is from (0,MAXLOCPRIOR).

<!--  Output options  -->
set_printnet_ = (Switch) Print the net nucleotide distance between clusters (PRINTNET)			
set_printqhat_= (Switch) default=0 When this is turned on, the point estimate for Q is not only printed into the main results file, but also into a separate file with suffix “q”. This file is required in order to run the companion program   STRAT.
set_ancestdist_ = (Switch) default=0 Collect information about the distribution of Q for each individual (ANCESTDIST)