Start GeneClass2 from your "Start" menu, folder "CBGP". The splash-screen appears, then the main window of GeneClass2.

Load a reference datafile by clicking on the upper "Open" button
[**H1**] and choose the datafile in
the selector.

Load a to-be-assigned individuals datafile by clicking on the lower "Open"
button [**H1'**] and choose the datafile
in the selector.

Note that for self-assignment purposes only a single file is needed (i.e. the
reference file [**H1**]) .

Choose "Assignment" [**H2**]
in the first tab of the main window and "Individuals" [**H3**]
in the "Assign:" box.

Note that assignment statistics can be also computed for groups of individuals
rather than individual genotypes (Baudouin
& Lebrun, 2000). Groups of individuals must be coded as populations
in the samples file.

The assignment threshold (without probability computation) can be set by sliding
the "Assignment threshold of scores" cursor [**H4**]
(see computations without associated probabilities section
for a definition of scores).

Click on the "2) Criteria for Computation" [**I1**]
tab and choose the desired criterion (e.g. "Rannala & Mountain"
[**I2**], see Rannala
& Mountain, 1997 and Cornuet *et
al.*, 1999). Bayesian and Frequencies-based methods appears to be better
than distance-based methods (see Cornuet *et
al.* 1999 for a comparative study).

If you want to compute the probability that an individual belongs to each reference
population, click on the "3) Probability computation" tab [**J1**],
and then check the "Enable probability computation (Monte-Carlo resampling)"
box [**J2**].

You can now choose a resampling algorithm [**J3**],
eg. Paetkau *et al.* (2004) (recommended,
but see Rannala & Mountain 1997 and
Cornuet *et al.* 1999). Slide the
cursor [**J4**] to define the minimum
number of simulated individuals (eg. 1000, default value or 10000, leading to
ten times longer but more precise computation), and the cursor [**J5**]
setting the type one error eg. 0.01, default value (see Cornuet
*et al.* 1999; Paetkau *et al.*
2004 ).

If needed, you can deselect some loci in the "Loci selection" tab
[**K1**]. Deselected loci will be
ignored during calculations.

Finally, click on the "Start" button [**K2**]
to run the computation.

The program displays the "Log file" [**L1**]
that displays the running parameters.

The progress bar and a counter shows the state of the computation [**L2**].

The "Stop" button [**L3**]
allows the computation to be aborted.

Once computations are finished, the results are displayed in a grid in which
the probability for each individual belonging to each reference population is
displayed [**M1**] (Cornuet
*et al.*, 1999). If a given individual's probability in a given reference
population is lower than the previously defined threshold, the value is greyed
[**M2**].

Results can be printed ("Print" button [**M3**])
or exported in csv format ("Export" button [**M4**]).

*Computations without associated probabilities:*

If you did not check the "Enable probability computation (Monte-Carlo
resampling)" box [**J2**] the
results are displayed as follows: The five first pairs of columns show, for
each individual, the most likely populations and their relatives scores (*cf.*
note below) in decreasing order [**N1**].
The right part of the grid displays -log values of the likelihoods [**N2**].

The number of displayed scores can be changed with the spin edit area [**N3**].

Note:In a reference file withkpopulations the score of an individualiin a populationlis computed as follow:,

with

Li,lthe likelihood value of the individualiin the populationl.