HAPPE: A Tool for Population Haplotype Analysis and Visualization in Editable Excel Tables

文献类型： 外文期刊

第一作者： Feng, Cong

作者： Feng, Cong;Wang, Xingwei;Wu, Shishi;Ning, Weidong;Song, Bo;Yan, Jianbin;Cheng, Shifeng;Wang, Xingwei;Wu, Shishi;Wang, Xingwei;Wu, Shishi;Ning, Weidong

作者机构：

关键词： haplotype; SNPs; phylogenetic clustering; visualization; Excel

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：6.627； 五年影响因子：7.255 ）

ISSN： 1664-462X

年卷期： 2022 年 13 卷

页码：

收录情况： SCI

摘要： 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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