HaploThread: a scalable desktop tool for efficient haplotype network inference and interactive visualization

This note introduces HaploThread, a user-friendly desktop software with a graphical user interface designed for constructing and visualizing haplotype networks. Developed in C++ using the Qt library, HaploThread integrates network visualization with multiple multithreaded haplotype construction algorithms-including McAN and fastHaN (which incorporates MSN, MJN, and TCS)-through a modular plugin architecture. It provides an intuitive workflow for building and visualizing haplotype networks from large-scale datasets, while also supporting functional extensions via plugins to facilitate the analysis of genetic variation and evolutionary relationships. HaploThread is released as open-source software under the GNU General Public License. Its source code and precompiled executables for Windows and macOS are freely available at https://ngdc.cncb.ac.cn/biocode/tool/BT007948 and https://github.com/git-xubo/HaploThread.