"This is a comment: input test at Feb 24th 2006"
"Seed to start coalescent simulations"
seed1	111

"print_matrixpol. 0: does not show DNA sequences. 1: DNA sequences in phylip format. 2: ms format (+mhits) 3: phylip excluding mhits"
"print_neuttest Calculates and prints neutral tests. 0: no calculatation. 1=avg+var 2=values/loci + avg+var"
"Using the sliding windows or liked loci, avg+var file is not very informative. Then use option 2"
print_matrixpol 	0
print_neuttest	1

"Basic parameters: For more than 1 locus separate the values with spaces or tabs"
"npop indicates the number of populations  studied"
n_iterations	100
n_loci	1
n_sites 	1000
n_samples 	20
npop	1

recombination	10
thetaw	5

"Likelihood option. set at 1 only if the likelihood value is required."
likelihood_line	0

"Heterogeneity for mutation and recombination rates is allowed at positions. the value of alpha must be given. 0 or less indicates that a uniform will be used. A value (0,inf) ia allowed, being close to zero extreme hotspot distribution, 1 an exponential distribution, and >100 close to uniform."
"invar_mut_sites indicates the number of sites that are considered invariable (it is used as a proportion)."
heter_rec_alphag	-1
heter_theta_alphag	-1
invar_mut_sites	-1

"mhits: in case of considering multiple hits type 1, otherwise 0"
"seed2: add in case of mhits"
"mhratio_sv is the ratio transition/transversion, s/v = 0.5 indicates no bias. The mutational bias must be defined for each locus. Otherwise will be assigned 0.5 by default."
"dist_out indicates the divergence, in 4No generations, of the studied species to the outgroup"
mhits  	0
seed2  	123
mhratio_sv  	0.5
dist_out  	8

"factor that correct each locus for population size considering the chromosomal dotation in relation to 4N: e.g., An autosomal locus is 1 (4N), a locus located in the X chromosome has a factor of 0.75 (3N)."
"in case recombination is supressed in males, set no_rec_males at 1, otherwise set at 0."
factorn_chr	1
no_rec_males		0

"to increase the speed of simulations, the user can eliminate recombination after a tlimit time (in 4N generations). tlimit 1 means that after 4N generations the recombination has a value of zero."
tlimit	1000

"To use in case of linked loci: 0 no calculation, 1 use this option with sliding windows, > 1 for a number of separated fragments."
"pos_linked: type the first and the last nt positions (the first nucleotide is zero), comma and the next locus."
"linked_segsites, linked_rm and linked_nhapl are used to fix a number of segregating sites, Rm and number of haplotypes, respectively, for each linked region. These options are only allowed when theta (fixed or distribution) is defined "
nlinked_loci   	0
pos_linked 	0
linked_segsites	0
linked_rm	0
linked_nhapl	0
"in case n_locilinked = 1"
displ  	0
window  	0


"in case the theta distribution is a gamma, set ifgamma at 1. In case using a uniform distribution of theta values, set range_thetant at 1."
"In case of using a uniform distribution: In order to limit the theta values to biologically realistic values, set range_thetant at 1 and specify the limits of the theta per nucleotide values and the same values will be used for all the loci studied."
"in case the theta distribution is a known gamma distribution, set ifgamma at 1 and include FOR EACH LOCUS (separated by spaces) the value of p and alpha parameters in relation to variation per locus (NOT per nucleotide). "
"correct_gamma multiplies the result of the gamma distribution for the indicated value"
range_thetant  	0
thetant_min 	0.0005
thetant_max 	0.05
ifgamma	0
alpha_gamma	0.0
p_gamma	0.0
correct_gamma	0.0

"in case the recombination distribution is a gamma, set ifgammar at 1. In case using a uniform distribution of R values, set range_rnt at 1."
"In case of using a uniform distribution: In order to limit the R values to biologically realistic values, set range_rnt at 1 and specify the limits of the R per nucleotide values and the same values will be used for all the loci studied."
"in case the R distribution is a known gamma distribution, set ifgammar at 1 and include FOR EACH LOCUS (separated by spaces) the value of p and alpha parameters in relation to variation per locus (NOT per nucleotide)"
"correct_gammar multiplies the result of the gamma distribution for the indicated value"
range_rnt  	0
recnt_min 	0.0005
recnt_max 	0.05
ifgamma	0
alpha_gammar	0.0
p_gammar	0.0
correct_gammar	0.0

"sfix_allthetas: use this parameter in case conditioning over S and given a distribution of theta values (otherwise 0). rmfix must be 1 when conditioning on Rm (and alternatively the number of haplotypes)."
sfix_allthetas  	0
mutations  	0
rmfix	0
Rm	2
nhapl	0

"in case sfix_allthetas or/and rmfix be 1(defined), the method for obtaining samples conditioning values must be defined using method_samp: 1 indicates RA."
method_samp	1

"WARNING: each model is incompatible with the others, with the exception of selection plus neutral stationary model and migration plus changes in population size."

"ifselection: in case of selection type 1, otherwise 0"
"selection, we need N (pop_size), 4Ns (pop_sel), sel_nt is the position of selected nt (negative values are allowed)"
"sinit is the time in 4N generations since the selective process finished. Negative values are allowed and indicate unfinished processes."
"In case of selection, the recombination parameter value means the recombination value for the studied region. the recombination value to the selected position is inferred from the proportion"
ifselection  	0
pop_size  	1E06
pop_sel  	2E04
sel_nt  	-10000
sinit  	0

"some subdivision parameters: define in case of more than one population"
"npop_sampled, set the number of pops studied for each locus"
"ssize_pop = sample size of each pop separated by spaces, comma and the next locus."
npop_sampled   	1
ssize_pop  	20

"Refugia parameters: refugia 1 if used, otherwise 0"
"npoprefugia: number of refugia"
"time_split: from present to past, time in 4N generations the present population joined from all refugia."
"time_scoal: from present to past, time in 4N generations the population was splitted in several refugia."
"factor_anc: relative population size of the ancestral population, where No is 1."
"freq_refugia: average frequency contribution of each refugia to the present population (separated by spaces or tabs)."
refugia	0
npoprefugia  	2
time_split	0.0140
time_scoal	0.0165
factor_anc	0.1
freq_refugia	0.5 0.5

"Define in case of refugia or subdivision:"
"mig_rate = 4NNm. In case of more than one population, migration is needed."
"factor_pop = Population size in relation to N. 1 means N for each population or refugia (separated by spaces or tabs)."
"ran_factor_pop: 1 indicates that the relative population size of each population or refugia is randomly chosen before each iteration. Otherwise 0"
"same_factor_pop: indicates that the relative population size of each population or refugia is fixed on 1 (where No = 1). Otherwise 0"
mig_rate  	0
factor_pop    	1 0.1
ran_factorpop  	0
same_factorpop 	0

"Changes in N: set nintn at 0 if is not used."
"iflogistic 1 indicates that a logistic curve is used, otherwise (iflogistic 0) the changes in N are instantaneous and only nrec is used (npast is useless in this last case)"
"in case logistic growth, ts can be defined: ts is only available for the FIRST event (from present) and indicates the curve of the growth; for example:"
"in case the first event has a duration 0.1 and ts=0.0, the logistic grow shows a typical sigmoidal curve, but if ts=0.05, the curve is starting in the middle (showing an exponential-like curve) but continues for 0.1 (!) No generations."
"nintn = number of events."
"nrec = relative pop size at the beggining of the event (recent)"
"npast = relative pop size at the end of the event (past)"
"tpast = duration of the event in 4N generations"
iflogistic	1
ts	0.0
nintn	0
nrec	1
npast	1
tpast	0.15

"Observed values for statistics"
"The first column indicates if Pvalues are calculated (1) or not (0)."
"After the first column, include the values of each locus, separated by spaces or tabs. A maximum precission of +- 1e-06 is used."
"With this option the probability to have an observed value higher or equal than the simulated values is calculated."
"Note that the anme of the statistics FD* and FF* are replaced by FDn and FFn, and D/Dmax and H/Hmax by D_Dmin and H_Hmin respectively."

TD_obs	0	-0.0494264
Fs_obs	0	-1.59676
FDn_obs	0	0.0200351
FFn_obs	0	0.0131718
FD_obs	0	0.0134
FF_obs	0	-0.00123657
H_obs	0	0.783333
B_obs	0	0.125
Q_obs	0	0.205882
ZA_obs	0	0.220047
Fst_obs	0	
Kw_obs	0	0.6
Hw_obs	0	0.946667
R2_obs	0	0.122479
S_obs	0	37
pi_w_obs	0	0
pi_b_obs	0	0
thetaWatt_obs	0	9.79884
thetaTaj_obs	0	9.54
thetaFW_obs	0	9.13
D_Dmin_obs	0	-0.0189366
H_Hmin_obs	0	0.012183
maxhap_obs	0	0.16
maxhap1_obs	0	0.2
Rm_obs	0	3

"In case likelihood_line 1, then a interval for coincidence of the observed value (+/- the value) is required."
TD_err	0
Fs_err	0
FDn_err	0
FFn_err	0
FD_err	0
FF_err	0
H_err	0
B_err	0
Q_err	0
ZA_err	0
Fst_err	0	
Kw_err	0
Hw_err	0
R2_err	0
S_err	0
pi_w_err	0
pi_b_err	0
thetaWatt_err	0
thetaTaj_err	0
thetaFW_err	0
D_Dmin_err	0
H_Hmin_err	0
maxhap_err	0
maxhap1_err	0
Rm_err	0
