THE FOLLOWING VALUES ARE PRE-DEFINED IN GENOMEPOP. THEREFORE IF THE CORRESPONDING PARAMETERS ARE NOT INCLUDED IN THE INPUT FILE THEN
THE DEFAULT VALUES WILL BE USED.

THE EXCEPTION IS THIS FIRST LINE WITH THE DEFAULT VALUES AS APPEAR:

Chromsize	Numcroms	Kmax	Numpops	Maxgen 	MutRate per haploid genome	Rec
0		1		1000	1	0		1.0e-6			0.0


THE ABOVE LINE MUST ALWAYS BE INCLUDED AT THE INPUT FILE WITH THE DESIRED 7 VALUES. THE DEFAULT Chromsize 0 is NOT VALID VALUE. 
SO, THE MINIMUM INPUT FILE FOR GENOMEPOP TO WORK APPROPRIATELY MUST INCLUDE JUST THIS LINE WITH ADEQUATE VALUES. 

*** NOTE THAT TO INCLUDE ANY LINE, THE IMPORTANT IS THE FIRST WORD WHICH IDENTIFIES THE LINE ***
*** IT IS ALSO NECESSARY THAT THE CORRECT NUMBER OF VALUES APPEAR BELOW E.G. 7 VALUES BELOW THE CHROMSIZE IDENTIFIER **


**** THE FOLLOWING ARE THE DEFAULT VALID VALUES PRE-DEFINED IN GENOMEPOP: ***** 

Biological Model
non-viral

codon model 	omega 
false			1.0


runs		diploid	constantMetapopSize
1		true		true

scale
1


format
phylip

sustitutionmodel 
JC2. This implies that the output format is genepop instead of phylip. However if model is set to 4 alleles (JC4 or GTR) the default output format is phylip.


migration rate
0.0

migrationModel
island


recurrentmut	 retromut 
false			false

Sample size 
20		

Haplotypes
false

number of samples	
1

coefsel	coefDom     beta      Epistasis
0.00		0.0	    0.5	      0


TO SEE HOW TO DEFINE OTHER OPTIONS NOT INCLUDED IN THE DEFAULT AS FOR EXAMPLE: 
DIFFERENT POPULATION SIZES, SELECTIVE SITES OR USER PROVIDED SEQUENCES JUST SEE THE HOWTO PAGE, THE PROVIDED EXAMPLES OR THE PDF MANUAL.




______________________________________________
Antonio Carvajal-Rodríguez 2008