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
11 0 2		* Extra outputs for LD(1) + Het(2) + Temporal(8) = 11. All 3 temporal methods, 3rd entry = 2: only for top 2 critical values: 0.1 and 0.05
1 		* Create CI
0 		* Random mating in LD, required because LD is included on first line
0 		* 0: no restriction on samples/population
0		* 0: no restriction on number of populations
1 5   		* Run with loci 1 - 5 only.
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
7 		* Extra Output Files for all. (No restriction on critical values, and no Tab-delimiter.)
0 		* No CI
0 		* Random mating in LD, required because LD is included on first line
100 		* process only up to 100 individuals per population.
2 2		* Only Population 2 is processed.
0		* No Loci to be removed.
input2.gen	* input file name
Test2.out	* main output
Y *************** Continuing next input *********** INPUT  3 ******************
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)
8  0  1		* Extra Output File. 2d number has no effect (because only one temporal), 3rd = 1: only for the top critical value 0.1
1 		* Create CI
0 		* 0: no limit on individuals/pop.
2		* Population range (up to population 2, so up to 2 populations are run)
0		* 0: no loci removed.
input1.dat	* input file
Test1.out*	* MAIN output file name ended by asterisk, so all outputs will be appended
Y *************** Continuing next input ************ INPUT  4 *****************
15  0  		* All Methods. 2nd number = 0: all temporals included (this is redundant)
0		* Number of critical values is 0, so there is no line for critical values
500 0 1		* Generations timeline for temporal. (Plan 1, census size = 500)
15  4  1	* 15: Extra Output Files for all; 4: Jorde/Ryman temporal method only; 1: top 1 Critical values, irrelevant because no positive critical value
1 		* Create CI
0 		* Random mating in LD, required because LD is included on first line
30 		* Limit to individual 30/pop
2  5		* from population 2 to population 5 (4 populations)
0		* 0: No loci to be removed.
input1.dat	* input file
Test1.out	* MAIN output file name same as previous one, so all outputs will be appended
Y *************** Continuing next input ************ INPUT  5 ****************
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
15 		* Extra Output File for all, no restriction on temporals, no restriction on critical values.
0 		* No CI created
0 		* Random mating in LD, required because LD is included on first line
0 		* 0: no limit on individuals/pop
0		* 0: no restriction on number of populations
1  4  8  10	* Loci 1-4, and 8-10 will be run.
input2.gen	* input file name - Input & Output are all in the same dir. as the executable
Test2.out*	* output file name ended by asterisk, so all outputs will be appended
Y *************** Continuing next input ************** INPUT  6 ***************
15  6		* 15: all methods. For temporal, 6 = 2(Nei/Tajima) + 4(Jorde/Ryman) methods
3		* 3 critical values
0.1  0.05  0.02	* Critical values
200 0 2		* Generation timeline for temporal. Plan I, with census size = 200
15  3		* Extra Output File for all. The second 3 for temporal Pollak(1) + Nei/Tajima(2), so only Nei/Tajima method is in extra output.
1 		* Create CI
0 		* Random mating in LD, required because LD is included on first line
0 		* 0: no limit on individuals/pop
0		* 0: no restriction on number of populations
6  		* only number 6 > 0 on this line, so only loci from 1 to 6 will be considered.
input1.dat	* input file
Test1.out*	* output file name ended by asterisk, so all outputs will be appended
Y *************** Continuing next input ***************** INPUT  7 *************
7		* 7 = All methods except temporal
3		* 3 critical values
0.1  0.05  0.02	* Critical values
7  0 0		* Extra Output File for all. The second entry (0) is for temporal, irrelevant because no temporal here, but is needed to have the 3rd entry: 0, which means extra output for critical value 0 only
1 		* Create CI
0 		* Random mating in LD, required because LD is included on first line
0 		* 0: no limit on individuals/pop
0		* 0: no restriction on number of populations
0		* 0: No loci to be removed.
input2.gen	* input file name
Test2.out*	* 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 "multiplus.txt"):
	  Ne2 m+:multiplus.txt	(Windows)
	./Ne2M m+:multiplus.txt	(Mac)
	./Ne2L m+:multiplus.txt	(Linux)
Prefix for the name of this file:
	Letter 'm' followed by plus sign '+' and a colon ':',
regardless of how this file is named.


General Instructions
--------------------
Each run may require up to 12 lines.
One line less if there is no temporal method (M < 8 on line 1).
One line less if no positive critical values (C = 0 on line 2).
One line less if no LD method (M is an odd number on line 1).
Thus, the minimum number of lines is 9.

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 (LD),
                  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.
         This line exists only if entry C on line 2 is positive.
         Critical value 0 will be automatically added to the list.
         To exclude value 0, enter "-1" 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  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 (no zero).
         * 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 on line 2.

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.

         To terminate a generation set, at least a white space (blank or tab)
         followed by an asterisk should be entered.

Line 5:  A number M+ to indicate if extra ouput files in tabular format will
         be written for any or all methods indicated on line 1.
         The value of M+ is constructed in the same way as M on line 1.
         If M+ = 0, no extra outputs will be written.

         * Note: If M+ indicates a method not included by M, that method will
         be ignored. For example, if M = 5 (LD and Molecular Coancestry), and
         M+ = 2 (Het-Excess), then no method will be outputted to extra files,
         the effect is the same as M+ = 0. Essentially, anything to be put
         in extra files must be included in the main output file.

         * If M+ includes temporal methods, then a second number T+ can be
         entered to indicate which temporal method(s) to be outputted in
         extra file. This T+ is interpreted the same way as T on line 1.
         Therefore, if T+ = 0, or is absent, all temporal methods for main
         output file will be in extra output file as well.
         
         However, if this T+ conflicts with T on line 1, in the sense that
         none of the methods it indicates is in the main output file, then
         the value of T+ will be ignored (as it is not entered or it is 0).
         
         For example, if M+ = M = 8, and T = 3 (Pollak and Nei/Tajima in the
         main output), but T+ = 4 (Jorde/Ryman), then this T+ conflicts with
         T, so will be ignored. As a result, Pollak and Nei/Tajima methods
         being in main output file will also be in extra output file.
         With the same example, but now T+ = 5 (Pollak and Jorde/Ryman), then
         it is not considered a conflict with T since it has Pollak method
         in common; so only Pollak method is in extra output file.

         * A third number C+ is entered for limitation on critical values
         outputted to all extra output files. To be a third, there must be a
         second on the line, which is T+, even no temporal output (T+ is
         then ignored but must be entered, such as T+ = 0).
         The number C+ is for the number of highest critical values outputted
         to extra files.
         For example, if positive critical values are 0.05, 0.02 (C = 2), and
         C+ = 1, then only critical value 0.05 is on all extra output files.

         If C+ = 0, only critical value 0 is on the extra output files.
         If C+ > C (number of POSITIVE critical values), or C+ is ABSENT,
         then all critical values, including 0, will be on extra output files.

         NAMES for EXTRA OUTPUT Files
         ----------------------------
         From the name of the main output file, the extension is removed to
         obtain the principal name, Then the following suffixes are added to
         the principal name to make the names for extra output files:

         * For LD, suffix = "xLD.txt"
         * For Het-Excess, suffix = "xHt.txt"
         * For Molecular Coancestry, suffix = "xCn.txt"
         * For Temporal, suffix = "xTp.txt"

         Examples: (All names are enclosed by double quotes.)
         (1) Suppose the main output is "main.out" or "main" (no extension).
             Then the principal name is "main"; so
               * Extra output file name for LD: "mainxLD.txt"
               * Extra output file name for Het-Excess: "mainxHt.txt"
               * Extra output file name for Molecular Coan.: "mainxCn.txt"
               * Extra output file name for Temporal: "mainxTp.txt"

         (2) Suppose the main output is "main.txt.out". Then the extension is
             "out", the principal name is "main.txt". So
               * Extra output file name for LD: "main.txtxLD.txt"
               * Extra output file name for Het-Excess: "main.txtxHt.txt"
               * Extra output file name for Molecular Coan: "main.txtxCn.txt"
               * Extra output file name for Temporal: "main.txtxTp.txt"

Line 6:  Enter 1 to have Confidence intervals created, 0 if not.

Line 7:  If LD method is included by entry M on line 1 (when M is odd), then
         this line is for mating model: enter 0 for Random, 1 for Monogamy.

Line 8:  A number S for the maximum number of individuals in each population
         to be processed, starting from the first individual.
         If S = 0, no restriction.

Line 9:  Either one number P or two numbers P, Q are entered to restrict
         the processing of populations in input file.
         If P <= 0: no restriction (Q if entered will be ignored).
         If P > 0 and no Q entered, then populations up to population P will
         be processed.
         If both P and Q are entered (they should be positive) and P <= Q,
         then populations to be processed will be in the range from P to Q.
         However, if P > Q, the second entry Q is erroneous, and is rejected,
         therefore, it is assumed only one entry P is entered.

         Note that when temporal is in place, then generation set should be
         applied starting from the first population in the range.

Line 10: Enter ranges of loci to be considered. Each range consists of two
         ascending numbers. If 0 (zero) is the first number on this line,
         then no restriction on loci.

Line 11: Input file name.
         If its extension is "gen", it must be in GENEPOP format.

Line 12: 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 - blank or tab - in front of the asterisk.)

         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.



