This option 5 provides information such as allele frequencies, genotype frequencies, Fis estimates for each allele following Weir and Cockerham (1984), global estimate of Fis according to Weir and Cockerham (1984) and Robertson and Hill (1984), and gene diversities. Previous versions of Genepop showed relatively little interest for gene diversities ('heterozygosities') per se. However, these computations turn out to be sometimes useful.
Suboption 2 allows one to compute multilocus heterozygosities per individual, which may be useful e.g. in studies of inbreeding depression. They will appear in the last table of the output file if your entered each individual as a 'sample', (separated by a 'Pop') in the input file. Suboption 3 will likewise return multilocus averages of the squared difference between the size of the two alleles of an individual.
Sub-option 1 - This option provides basic information on the data set.
For each locus in each sample, several parameters are calculated:
In this web version of Genepop, summary tables for each population and for each locus
are provided. A table of allele frequencies for each locus and for each sample is also computed.
Sub-option 2 - This option computes diversity within individuals ('1-Qintra'), and among individuals within samples ('1-Qinter') per locus per sample, and averaged over samples or over loci. Corresponding Fis estimates are also computed. This option takes the observed frequencies of identical pairs of genes as estimates ( 
) of corresponding probabilities of identity ( 
) and then simply computes diversities as 
. Of course, no estimate is given when no information is available (e.g. no estimate of diversity between individuals within a sample when only one individual has been genotyped).
Sub-option 3 - Option 5.3 is analogous to option 5.2. This option computes measures of diversity based on allele size, namely mean squared allele size differences within individuals ('MSDintra'), and among individuals within samples ('MSDinter'), per locus per sample, and averaged over samples or over loci. Corresponding Rho_is estimates are also computed. This option assumes that allele size corresponds to the allele entries in the data file. See Option 6, suboptions 3 and 4, for details. Although statistics based on allele size are somehow fashionable, we do not advise their systematic use
For all suboptions, results are returned via your web browser which you can then save to you local machine. You may also choose to have them emailed to you.
Please report any problems are bugs that you encounter with the web version of this option to Eleanor Morgan