Advanced Haplotype Frequency Calculator

Enter Haplotype Data

Add one haplotype per line using the selected delimiter. Example: A-B,40

Delimiter

Decimal Places

Minimum Count Filter

Sort Results By

Chart Type

Haplotype Data

Example Data Table

Haplotype	Observed Count	Meaning
A-B	40	Most common combined allele pattern in the sample.
A-b	25	Moderately frequent haplotype across sampled individuals.
a-B	20	Alternative allele combination with notable presence.
a-b	15	Least frequent example haplotype in this dataset.

Formula Used

Haplotype Frequency:

f_i = c_i / Σc

Percentage:

%_i = f_i × 100

Shannon Entropy:

H = -Σ(p_i ln p_i)

Simpson Diversity:

D = 1 - Σ(p_i²)

Effective Haplotype Number:

N_e = 1 / Σ(p_i²)

Here, c_i is the observed count for one haplotype, and p_i is its normalized frequency.

How to Use This Calculator

Enter haplotypes and observed counts in the textarea.
Select the delimiter matching your input format.
Set decimal places and an optional minimum count filter.
Choose how to sort the final haplotype table.
Pick a bar chart or pie chart view.
Click Calculate Frequencies to see results above the form.
Review totals, diversity metrics, frequencies, and cumulative percentages.
Download the computed table as CSV or PDF.

FAQs

1. What does this calculator measure?

It converts observed haplotype counts into normalized frequencies, percentages, and diversity summaries. This helps you compare how common each haplotype is within one sampled dataset.

2. Can I enter any haplotype label format?

Yes. Labels can be letters, numbers, or paired markers such as A-B, H1, or 101-202. The first field is treated as a name, and the second field is treated as the count.

3. Does this estimate phased haplotypes from raw genotypes?

No. This version assumes haplotype counts are already observed or derived elsewhere. It summarizes frequency distributions rather than performing phase reconstruction or EM-based estimation from ambiguous genotypes.

4. Why use Shannon entropy here?

Shannon entropy shows how evenly haplotypes are distributed. Higher values suggest less dominance by a single haplotype and greater overall diversity across the sample.

5. What does Simpson diversity show?

Simpson diversity reflects the chance that two randomly chosen observations belong to different haplotypes. Larger values usually indicate a more balanced frequency structure.

6. What is the effective haplotype number?

It converts uneven frequency patterns into an equivalent number of equally common haplotypes. This makes diversity easier to compare across different datasets or populations.

7. Can I remove rare haplotypes from the analysis?

Yes. Use the minimum count filter to exclude very small observations. That is useful when you want cleaner summaries or when rare entries reflect noise.

8. What download options are included?

You can export the calculated result table as a CSV file for spreadsheets or create a PDF report for sharing, printing, and documentation.