HELP WITH GENEPOP

Contents

Input Files


Output Files

The data file for GenePop(WWW) and LinkDos(WWW) should be typed or pasted into the Text Window provided.

"ind#001fem," is an identifier for your personal use. You can use any character, including a blank space or tab. This now follows the original Genepop file format which allows spaces in the identifier names. You may leave it blank except for a comma if you wish. The first identifier of every sub-population is used by Genepop(WWW) in all output files to name populations; the DOS version of Genepop takes the last identifier of each population to name populations. The comma between the identifier and the list of genotypes is required.

Genotypes for each locus are separated by one or more blank spaces. 0101 indicates that this individual is homozygous for the 01 allele at the first locus. The same individual is homozygous for the 02 allele at the second locus (0202).

Data is missing at the third locus (0000). At the fourth locus, the gen0type is 0410, which indicates the presence of allele 04 and 10. To indicate the next population, use the word "Pop" like in Line N+2.

An example of a short input file is given below :

------------- The file starts here ---------------- 
Microsat on Chiracus radioactivus, a pest species 
     Loc1, Loc2, Loc3, Y-linked, Loc4 
POP 
AA8, 0405 0711 0304 0000      0505 
AA9, 0405 0609 0208 0000      0505 
A10, 0205 0609 0101 0000      0305 
A11, 0405 0606 0102 0000      0504 
A12, 0202 0609 0105 0000      0507 
A13, 0505 0909 0107 0000      0505 
A14, 0202 0609 0207 0000      0503 
A15, 0405 0609 0101 0000      0505 
Pop
AF, 0000 0000 0000 0000      0505 
AF, 0205 0307 0102 0000      0505 
AF, 0202 0609 0202 0000      0505 
AF, 0205 0909 0000 0000      0505 
AF, 0205 0307 0202 0000      0505 
AF, 0505 0303 0102 0000      0505 
AF, 0205 0700 0000 0000      0505 
AF, 0505 0900 0000 0000      0405 
AF, 0205 0600 0000 0000      0505 
AF, 0505 0606 0202 0000      0505 
pop 
C45, 0505 0606 0202 0000      0505 
C45, 0505 0909 0202 0000      0505 
C45, 0505 0306 0202 0000      0505 
C45, 0505 0909 0102 0000      0405 
C45, 0205 0303 0202 0000      0505 
C45, 0205 0909 0202 0000      0405 
------------- The file ends here -------------------

An alternative input format exists, where each allele is coded by three digits (instead of two as described above). However, the total number of different alleles, for each locus, should not be higher than 99. An example of such three-digits input file is given below.

________the file starts below this line_____________
Title line: "Mosquito populations in southern France"
MicroSat 1
Microsat 2
Est-3
Pop
RueDuQuai    ,  250230 564568 110100
RueDuQuai    ,  252238 568558 100120
RueDuQuai    ,  254230 564558 090100
RueDuQuai    ,  250230 564568 110100
RueDuQuai    ,  252240 568558 100120
RueDuQuai    ,  254230 564558 090090
Pop
Benitier     ,  254230 564558 080100
Benitier     ,  000230 564558 090080
Benitier     ,  254230 000000 090100
Benitier     ,  254230 564000 090120
_________the file ends above this line___________

This format can be used to conveniently record genotypes of electrophoretic or of some microsatellite loci. The length (in nucleotides) of a microsatellite (loci 1 and 2 in the example above) or the relative mobility of electrophoretic alleles (3rd locus) can be directly indicated. This format makes it easier to check the input file for mistakes. Missing data are indicated as " 000 ", as illustrated in the second population of the above file. Note that the homozygote for the 90 allele is noted 090090 (and not 9090 as in the two digit format).

To use this input file you must choose the 3-Digit Alleles option above the input text box on the Genepop Data Form, then paste or type the data into the text box provided. The web version of Genepop will work for all options with data in the 3-Digit format without the need to convert the file to a 2-Digit format. However, you may wish to to convert your file to a 2-digit format for use with the Dos version of Genepop, a utility to do this conversion is available under Option 8.3.

Note :

• No constraint on blanks separating the various fields, tabs or spaces allowed.
  
• Loci names can appear on separate lines, or on one line if separated by spaces or tabs
• Individual identifier may have blanks but must end with a comma
  
• The web version of Genepop takes the first identifier in the population as the population name.
• Alleles are numbered from 01 to 99 (or 001 to 999). Consecutive numbers to designate alleles are not required.

• Populations are defined by the position of the "Pop" separator. To group various populations, just remove relevant "Pop" separators.

• Genotypes can extend on more than one line.
  
• Missing data should be indicated as 00 (or 000) rather than blanks. There are three possibilities for missing data :
  • no information (0000) or (000000),
  • partial information for first allele (1000) or (010000),
  • partial information for second allele (0010) or (000010).

• The number of locus names should correspond to the number of genotypes in each row. If you remove one or several loci from your input file, you should remove both their names and the corresponding genotypes.

• No empty lines should be found within the file.
  
• No more than one empty line should be present at the end of file.
  

There are 2 methods for returning the results after processing

1) Email the results. Address :

Allows you to enter an email address where the results of processing the Genepop data (in text format) will be sent to.. You can enter the desired email address in the text box provided.

2) HTML :

It is possible to view the output via the Web in the following formats :

• Text Only
  Presents data in text only format, suitable for saving to disk as a text file for printing.
• Graphically Enhanced (will be implemented soon)
  Displays results as html tables and includes bar graphs of data where appropriate for a more effective visual representation of the results.