15		* All methods, the temporal methods include all three: Pollak, Nei/Tajima, Jorde/Ryman.
3		* 3 positive critical values, critical values will be listed on next line
0.1  0.05  0.02	* All 3 positive critical values.
0 0 1		* Plan II for temporals. Generations are 0, 1 applied to all populations
input1.dat	* Input file.
Test1.out	* Main output file name.
y *************** first char must be 'y' (case insensitive) for continuing next input, else: stop. INPUT 2
7		* 7 = all methods except temporal: there should be no line for generations
3		* 3 positive critical values for rare alleles.
0.1  0.05  0.02	* All critical values as said on previous line
input2.gen	* input file name
Test2.out	* main output
Y *************** Continuing next input ************ INPUT  3 ****************
15		* 15: all methods.
3		* 3 critical values
0.1  0.05  0.02	* Critical values
0 0 1		* Generation timeline for temporal. Plan II, generations 0, 1 applied to all
input2.gen	* input file name - Input & Output are all in the same dir. as the executable
Test2.out	* output file name, same name as previous one, so all outputs will be appended
Y *************** Continuing next input *********** INPUT  4 ******************
8  2		* 8 = Temporal methods only. Second number 2 = Nei/Tajima; so only Nei/Tajima temporal method is run
3		* 3 critical values.
0.1  0.05  0.02	* Critical values
200 0 1		* Generations for temporal. (Plan I, Census size = 200)
input1.dat	* input file
Test1.out*	* MAIN output file name ended by asterisk, so all outputs will be appended
q *************** The first letter is neither 'y' nor 'Y',
		  the program stops reading this file.

To run Ne2 with this file, open a terminal at the directory containing the
executable Ne2, this file, and all input files mentioned in this file.
Then issue command line (assuming this file is named "multi.txt"):
	  Ne2 m:multi.txt	(Windows)
	./Ne2M m:multi.txt	(Mac)
	./Ne2L m:multi.txt	(Linux)
(prefix for the name: letter 'm' followed by a colon ':').


General Instructions
--------------------
This type of running multiple files assumes the default settings:
* LD method will be Random Mating model,
* Temporal methods are in Plan II,
* All Confidence Intervals will be outputted,
* No restriction on loci or populations or number of individuals,
* No outputs in tabular format.

Each run requires up to 6 lines.
One line less if there is no temporal method (M < 8 on line 1).

Each line can be terminated by a white space (blank or tab) followed by an
asterisk (then comments can be put on the line after the asterisk).
The asterisk is optional except for the line reserved for "generation set"
in temporal methods. Note that the asterisk should be after a white space,
unless at the line for output file name, where the asterisk will play a role.


Line 1: A number M from 1 to 15 to indicate which method(s) to run:
                 M = 1 for Linkage Disequilibrium method,
                 M = 2 for Heterozygote Excess method,
                 M = 4 for Molecular Coancestry method,
                 M = 8 for Temporal methods.

        For multiple methods, M is the sum of the designated method numbers.
        Examples: M = 3 = LD + Het-Excess; M = 9 = LD + Temporals.

        A second number T can be entered to indicate which temporal method(s)
        to run (if temporal is indicated by entry M >= 8). T can be any
        number at least 0.
        * If T = 0, or T is at least 7, or T is absent, then all temporal
          methods are included. If T is absent, there should be a non-digit
          character, e.g. an asterisk, following at least a blank after entry M.
        * If 1 < T < 7, then T is one or is the sum of two of the following:
          1 (Pollak method), 2 (Nei/Tajima method), 4 (Jorde/Ryman method).
          The temporal method(s) to run will be the ones corresponding to
          the number(s) included in T. This is similar to how M is designated.
        (If M < 8, i.e., no temporal methods, then T is ignored if entered.)

Line 2: A number C for the number of POSITIVE critical values. If C > 0, the
        next line should list all C critical values. If C = 0, there should be
        no line for critical values. (Molecular Coancestry method will
        ignore all positive critical values. But even if M = 4 on line 1,
        i.e., only Molecular Coancestry being run, the list of critical
        values must be entered on the next line if C > 0 is entered here.)

Line 3: Lists all positive critical values as said on line 2.
        Critical value 0 will be automatically added to the list.
        To exclude value 0, enter -1 (minus one) after the last critical value.
        If -1 is inserted after any value listed here, the list will stop
        at that value, regardless of the value of C.
        Examples. Suppose C = 3.
        * If line 3 consists of
        	0.05  0.02  0.01
          then list of critical values is 0.05, 0.02, 0.01, and 0.
        * If line 3 consists of
        	0.05  -1  0.02  0.01 -1
          then list of critical values is 0.05, 0.02, 0.01 (no zero).
        * If line 3 consists of
        	0.05  -1  0.02  0.01
          then list of critical values is 0.05.
        * If line 3 consists of
        	-1  0.05  0.02  0.01
          then the list of critical values consists of only 0, the effect is
          the same as C = 0.

Line 4: For "Generation Set" in Temporal methods when M on line 1 is
        at least 8. A generation set consists of a number N followed by
        at least two ascending numbers for generations (these numbers can
        have decimals). The generation set applies to the whole input file.
        If N = 0, temporal method(s) will assume Plan II.
        If N > 0, then temporal method(s) will assume Plan I and N is
        the census population size.

Line 5: Input file name.
        If its extension is "gen", it must be in GENEPOP format.

Line 6: Main Output file name. In general, the file if existed will be
        overwritten. It will be appended if one of the following takes place.
        
        * It has the same name as the output file of the preceding run.
          (Important note: the names are compared with CASE-SENSITIVE.)
        * The name is ended by an asterisk (no white space between).

        NOTE: If the main output is overwritten or appended, then all extra
        output files will also be in the same mode.

After the line for main output file name, if the next line starts with letter
'Y' (case insensitive), then it is expected there will be another run.
Therefore, to terminate, enter something else as first character on the line.




