I am not an expert in this field, but I am very interested and have researched to find an answer. I received some assistance from tlooto.com for this response. Could you please review the response below to see if it is correct?

To analyze ISSR data for Tamarindus indica using STRUCTURE software, follow these steps:

1. Data Preparation: Convert your ISSR data into a binary matrix (presence/absence of bands) suitable for STRUCTURE. Each band is coded as 1 (present) or 0 (absent) [1][2].

2. Input File Creation: Format the binary matrix into the STRUCTURE-specific input file (.str). This file should include sample IDs and loci information [3][4].

3. Parameter Settings: Launch STRUCTURE and set the following parameters:

• Burn-in Period: Typically 10,000 to 50,000 iterations based on dataset complexity.
• MCMC Repetitions: 50,000 to 100,000 iterations after burn-in for accurate estimates.
• Number of Populations (K): Test multiple K values to determine the optimal number of clusters [5][6].

4. Run Analysis: Perform the analysis with multiple independent runs for each K value to ensure consistency. This helps in identifying the most stable clustering solution [7][8].

5. Result Interpretation: Use STRUCTURE's output to determine the genetic structure and diversity within your Tamarindus indica samples. Visualize the results using the software's graphical tools or external programs like STRUCTURE HARVESTER for better interpretation [9][10].

By following these steps, you can effectively analyze the genetic diversity and population structure of Tamarindus indica using ISSR markers in STRUCTURE software.

Reference

[1] Yan, W., Li, J., Zheng, D., Friedman, C., & Wang, H. (2019). Analysis of genetic population structure and diversity in Mallotus oblongifolius using ISSR and SRAP markers. PeerJ, 7.

[2] Salameen, F. A., Habibi, N., Kumar, V., Amad, S. A., Dashti, J., Talebi, L., & Doaij, B. A. (2018). Genetic diversity and population structure of Haloxylon salicornicum moq. in Kuwait by ISSR markers. PLoS ONE, 13.

[3] Guizado, S. J. V., Nadeem, M., Ali, F., Barut, M., Habyarimana, E., Gómez, T. P., Santillan, J. A. V., Canales, E., Gómez, J. C. C., Chung, G., & Baloch, F. (2020). Genetic diversity and population structure of endangered rosewood from the Peruvian Amazon using ISSR markers. Acta Amazonica, 50, 204-212.

[4] Santos, L., Ferrer, M. M., Ruenes-Morales, M. R., Montañez-Escalante, P., Andueza-Noh, R., & Jiménez-Osornio, J. (2020). Genetic diversity and structure analysis of Vigna unguiculata L. (Walp.) landraces from southeastern Mexico using ISSR markers. Plant Genetic Resources: Characterization and Utilization, 18, 201 - 210.

[5] Mohsenzadeh, S., Sheidai, M., & Koohdar, F. (2019). Population genetic structure in Plantago ovata var. decumbens with using ISSR markers. Genetika.

[6] Qahtan, A. (2021). Genetic Diversity and Structure Analysis of a Worldwide Collection of Faba bean (Vicia faba) Genotypes using ISSR Markers. International Journal of Agriculture and Biology, 25, 683-691.

[7] Emegha, F. E., Animasaun, D. A., Bankole, F., & Olaoye, G. (2021). Analysis of genetic diversity in selected sugarcane (Saccharum officinarum L.) accessions using inter simple sequence repeat (ISSR) markers. Acta agriculturae Slovenica.

[8] Costa, J. C., Fracetto, G., Fracetto, F., Souza, T. C., Santos, M. V. F., & Junior, M. A. L. (2018). Genetic diversity in natural populations of Stylosanthes scabra using ISSR markers. Genetics and Molecular Research, 17.

[9] Das, A., Gaur, M., Barik, D., & Subudhi, E. (2017). Genetic diversity analysis of 60 ginger germplasm core accessions using ISSR and SSR markers. Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology, 151, 822 - 832.

[10] Rajasekharan, P., Kareem, V., Ravish, B., & Mini, S. (2016). Analysis of Genetic Diversity in Alpinia galanga using ISSR Markers. Indian Journal of Plant Genetic Resources, 29, 194-198.

Thank you so much brother...

I used STRUCTURE software to identifiyof interspecific hybrids between pearl millet (Pennisetum glaucum [L.] R.Br.) × napier grass (Pennisetum

purpureum Schumach). I think the protocol is given by Park Sowon is correct for your study you can also refer my citation for your work

Hello! could you solve this? I´m doing the same with T. frezii. Let me know if you have any specific issue, I´ll try to answer

Yes i did sturucture analysis for ISSR marker data