Journal
FRONTIERS IN PLANT SCIENCE
Volume 13, Issue -, Pages -Publisher
FRONTIERS MEDIA SA
DOI: 10.3389/fpls.2022.927407
Keywords
haplotype; SNPs; phylogenetic clustering; visualization; Excel
Categories
Funding
- National Key Research and Development Program of China [2019YFA0707003]
- Guangdong Innovation Research Team Fund [2014ZT05S078]
- Guangdong ZhuJiang Talent Innovation project [2019ZT08N628]
- NSFC Excellent Young Talent [32022006]
- special funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District [PT202101-01]
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Haplotype identification, characterization, and visualization are crucial in population genomics. HAPPE is a user-friendly tool that uses coloring of Excel tables to display genotypes and haplotypes, along with additional information such as phylogenetic trees and GWAS values.
Haplotype identification, characterization and visualization are important for large-scale analysis and use in population genomics. Many tools have been developed to visualize haplotypes, but it is challenging to display both the pattern of haplotypes and the genotypes for each single SNP in the context of a large amount of genomic data. Here, we describe the tool HAPPE, which uses the agglomerative hierarchical clustering algorithm to characterize and visualize the genotypes and haplotypes in a phylogenetic context. The tool displays the plots by coloring the cells and/or their borders in Excel tables for any given gene and genomic region of interest. HAPPE facilitates informative displays wherein data in plots are easy to read and access. It allows parallel display of several lines of values, such as phylogenetic trees, P values of GWAS, the entry of genes or SNPs, and the sequencing depth at each position. These features are informative for the detection of insertion/deletions or copy number variations. Overall, HAPPE provides editable plots consisting of cells in Excel tables, which are user-friendly to non-programmers. This pipeline is coded in Python and is available at .
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