Haplotype Analysis
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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.

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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:
  1. 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.
  2. 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.
  3. 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)
  4. Providing your own list of Haplotypes in a tabulated format. This list should have the following format:

    Sample1    Hap1 Hap2
    Sample2    Hap1 Hap2
    ...          ...  ...

NOTE:
* 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 Results section.

There will be a *.zip file containing:

- haplotype_analysis.txt
Arlequin input file.

- All the output files that Arlequin has generated during its execution

- Analysis.txt
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 populations where:

    N
Number of chromosomes

    S
Number of polimorphic SNPs

K
Number of different haplotypes

H/ds(H)
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 populations.

- FST among populations

- SNPs.txt
A text file containing the list of SNPs that have been used to build the phase input file. It contains:

- SNP code
- Position
- Distance to next SNP

- arlequinProcess.log
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.

- Information.txt
General information about dates and times of performance, user, study, filters applied and other data

References:
  • 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.