This option allows the user to perform a population-based analysis of a set of
haplotypes using the Arlequin Software*. SNPator will take the set of
haplotypes and using information of the Samples Table will create an Arlequin file. SNPator runs Arlequin, takes the output and parses it to
create a results file with selected information.
The proper procedure is as follows:
1. Enter a Description to identify the process in the top box.
2. Select the haplotype list, there are four ways to do that:
Using genotypes already stored SNPator. This option is only valid
when all genotypes are haploid since in this case a set of genotypes is
equivalent to a haplotype.
- Selecting a PHASE* file previously produced in SNPator and stored in
the User Results section. You only have to select the result that you
want in the list.
- Providing a "report" file (one of the outputs of the Phase program) that
may be stored in your local computer. A "report.bis" file generated by
SNPator can be also used in this seccion. (More info about "report.bis"
files in Run PHASE help)
- Providing your own list of Haplotypes in a tabulated format. This list
should have the following format:
Sample1 Hap1 Hap2
Sample2 Hap1 Hap2
... ... ...
* missing alleles inside a haplotype must be entered as '?'
* haploid samples will have no "Hap2"
3. Determine by which fields of the Samples Table (if any) the groupings
have to be organized. First level will be treated as "Population" and Second
level as "Groups of populations".
4. The option "Input file Only" generates the Arlequin input file but do not run
it, in case you are interested in running it manually by yourself.
5. Finally, when the "Go" button is clicked, the results will be sent to the User
There will be a *.zip file containing:
Arlequin input file.
- All the output files that Arlequin has generated during its execution
File containing all the haplotype analysis information parsed
from the outputs of Arlequin. It contains:
- Haplotype counts and frequencies per population
- Descriptive statistics of the distribution of haplotypes per
Number of chromosomes
Number of polimorphic SNPs
Number of different haplotypes
Haplotipic diversity / standard deviation
(Referred as "Gene diversity" in Arlequin documentation)
Pi / ds(Pi)
Nucleotide diversity / standard deviation
- AMOVA analysis of the distribution of haplotypes per
- FST among populations
A text file containing the list of SNPs that have been used to
build the phase input file. It contains:
- SNP code
- Distance to next SNP
It is a log of the messages that Arlequin shows during execution.
Corresponds to what users would see on their screens if they
executed Arlequin on their workstation.
General information about dates and times of performance,
user, study, filters applied and other data
Stephens, M., Smith, N., and Donnelly, P. (2001). A
new statistical method for haplotype
reconstruction from population data. American Journal of Human Genetics, 68, 978--989.
Schneider, S.,Roessli, D., and Excoffier, L. (2000) Arlequin: A software for population
genetics data analysis. Ver 2.000. Genetics and Biometry Lab, Dept. of Anthropology,
University of Geneva.
- Stephens, M., and Donnelly, P. (2003). A comparison of Bayesian
methods for haplotype
reconstruction from population genotype data. American Journal of Human Genetics,