### VIEWpoly Citation

Taniguti, C. H., de Siqueira Gesteira, G., Lau, J., da Silva Pereira, G., Zeng, Z.-B., Byrne, D., Riera-Lizarazu, O., & Mollinari, M. (2022). VIEWpoly: a visualization tool to integrate and explore results of polyploid genetic analysis. Journal of Open Source Software, 7(74), 4242. https://doi.org/10.21105/joss.04242

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### Genetic Mapping Software

Please cite the appropriate genetic mapping software used:

#### MAPpoly

Mollinari, M., & Garcia, A. A. F. (2019). Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models. G3: Genes|Genomes|Genetics, 9(10), 3297–3314. https://doi.org/10.1534/g3.119.400378

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#### polymapR

Bourke, P. M., van Geest, G., Voorrips, R. E., Jansen, J., Kranenburg, T., Shahin, A., Visser, R. G. F., Arens, P., Smulders, M. J. M., & Maliepaard, C. (2018). polymapR—linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. Bioinformatics, 34(20), 3496–3502. https://doi.org/10.1093/bioinformatics/bty371

##### OneMap

Taniguti, C. H., Taniguti, L. M., Amadeu, R. R., Lau, J., Gesteira, G. de S., Oliveira, T. de P., Ferreira, G. C., Pereira, G. da S., Byrne, D., Mollinari, M., Riera-Lizarazu, O., & Garcia, A. A. F. (2022). Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps. GigaScience, 12. https://doi.org/10.1093/gigascience/giad092

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### Reporting Genetic Map Results

When publishing genetic maps visualized in VIEWmap:

**Include**:
1. VIEWpoly citation for visualization
2. MAPpoly, polymapR, or OneMap citation for map construction
3. Population type and size
4. Ploidy level
5. Number of markers and linkage groups
6. Total map length
7. Average marker spacing

**Map Quality Metrics**:
- Segregation distortion patterns
- Missing data percentage
- Largest gaps between markers
- Heat map of recombination fractions (if available)

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### Additional Resources

**MAPpoly Tutorial**: [https://mmollina.github.io/MAPpoly/](https://mmollina.github.io/MAPpoly/)

**polymapR Manual**: [https://cran.r-project.org/web/packages/polymapR/](https://cran.r-project.org/web/packages/polymapR/)

**OneMap Documentation**: [https://cran.r-project.org/web/packages/OneMap/](https://cran.r-project.org/web/packages/OneMap/)

**VIEWpoly Tutorial**: [https://cristianetaniguti.github.io/viewpoly_vignettes/](https://cristianetaniguti.github.io/viewpoly_vignettes/)

**Breeding Insight**: [https://www.breedinginsight.org](https://www.breedinginsight.org)
