HELP WITH GENEPOP

Input Files

Output Files

Input

The data file for GenePop(WWW) and LinkDos(WWW) can be uploaded, or can be typed or pasted into the Text Window provided. If uploaded, the datafile MUST be in plain text format.

The Input File Format for Genepop(WWW) and LinkDos(WWW) :

First line : Any characters. Use this line to store information about you data.
Second line : the name of the first locus.
Third line : the name of the second locus (if needed)
ETC...

Alternatively, separate loci with commas (or a comma+space) on the same line.
Line N+1 : the name of the Nth locus.
Line N+2 : Type the word "POP" (or "Pop", or "pop").
Line N+3 : And example is given below :

ind#001fem, 0101 0202 0000 0410

"ind#001fem," is an identifier for your personal use. You can use any character, including a blank space or tab. Spaces are allowed in the identifier names. You may leave it blank except for a comma if you wish. The last identifier of every sub-population is used by Genepop in all output files to name populations, except for the web version of option 7 (format conversions) and LinkDos, which will use the first identifier to name the population. 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 genotype 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).

The latest version of Genepop (4.0) allows a mixture of 2-Digit and 3-Digit allele sizes. It also allows a mixture of haploid and diploid data in the same datafile. All options of the current web version use Genepop 4.0 EXCEPT option 7 (file format conversions), option 6.9 (Isolde) and LinkDos. Option 7 and LinkDos require consistency with allele size and will only process diploid datafiles. Isolde requires a different file format altogether (see option 6 help).

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 commas
Individual identifier may have blanks but must end with a comma
The web version of Genepop now takes the last identifier in the population as the population name except for option 7.
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.
Individual genotypes for the web version must be on one line. This differs from the PC version.
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.

Output Results

There are 2 methods for returning the results after processing

1) Email the results :
Genepop results will be sent via email. Be sure to enter a valid email address in the text box provided (e.g : emorgan@curtin.edu.au). If EMAIL is the only option selected, your request will be placed in a queue. This is processed on a First Come First Serve basis. Long-running jobs ahead of you could slow down the processing of your results. If you have not received your results within 24 hours, you should contact the server administrator, Eleanor Morgan.

2) HTML :
Results will be returned via the web browser in text format as returned by the Genepop software. If the analysis exceeds 10 minutes, the web page will time out. In that case, you should have your results returned by email only. Note that if you select both EMAIL and HTML for the output, your email request will NOT be placed in the email queue but will be returned as soon as the result is returned via the web browser.

This page was last modified on September 25, 2009

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HELP WITH GENEPOP

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Input Files

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