CandiHap A haplotype analysis toolkit for natural variation study


Haplotype blocks greatly assist association-based mapping of casual candidate genes by significantly reducing genotyping effort. The gene haplotype, which could be used to evaluate variants of affected traits captured from the gene region. While there is a rising interest in gene haplotypes, much of the corresponding analysis was carried out manually. CandiHap allows rapid and robust haplotype analysis and candidate identification preselection of candidate causal SNPs and InDels from Sanger or next-generation sequencing data. Investigators can use CandiHap to specify a gene or linkage sites based on GWAS and explore favorable haplotypes of candidate genes for target traits. CandiHap can be run on computers with Windows, Mac, or UNIX platforms in a graphical user interface or command line, and applied to any species, such as plant, animal and microbial. The CandiHap software, user manual, and example datasets are freely available at BioCode: or GitHub:


  1. CandiHap: a haplotype analysis toolkit for natural variation study
    Cite this
    Xukai Li, Zhiyong Shi, Jianhua Gao, Xingchun Wang, Kai Guo., 2023/3/15 - Molecular Breeding
    Cited by (Google Schoolar as of April 17, 2023)


  1. Xukai Li

    College of Sciences, Shanxi Agricultural University, China

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xuk*** (June 9, 2020)
xuk*** (August 18, 2021)
Tool TypeToolkit
CategoryVariant effect prediction
PlatformsLinux/Unix, MAC OS X, Windows
TechnologiesPerl, Python2, R
User InterfaceDesktop GUI, Terminal Command Line
Input DataVCF
Latest ReleaseV1.3.0 (June 9, 2020)
Download Count35712
Submitted ByXukai Li

This work has been supported by the National Key R&D Program of China [2022YFC3400300]; the National Natural Science Foundation of China [32001608]; the Major Special Science and Technology Projects in Shanxi Province [202101140601027]; the National Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding (in preparation) [202204010910001-02].