CandiHap A haplotype analysis toolkit for natural variation study


CandiHap allows fast and robust haplotype analyses and candidate identification preselection of candidate causal variations from sequencing data. Investigators can use CandiHap to specify a gene or linkage sites based on GWAS and explore favourable haplotypes of candidate genes for target traits. CandiHap can be run on Windows or UNIX platforms in graphical user interface or command lines, and applied to any species of plant, animal and microbial.


  1. CandiHap: a toolkit for haplotype analysis for sequence of samples and fast identification of candidate causal gene(s) in genome-wide association study
    Xukai Li, Zhiyong Shi, Qianru Qie, Jianhua Gao, Xingchun Wang, Yuanhuai Han, 2020/2/28 -


  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 Count31657
Submitted ByXukai Li

This work was funded by the Youth Fund Project on Application of Basic Research Project of Shanxi Province (201901D211362), the Scientific and Technological Innovation Programs of Shanxi Agricultural University (2017YJ27 and 2018YJ31), Graduate Education Innovation Project of Shanxi Province (2019SY228), and Shanxi Key R&D Program (201703D211008).