biostudies-literatureUnknownLi LStrategic Priority Research Program of the Chinese Academy of SciencesYouth Innovation Promotion Association of CASBeijing Nova ProgramNational Natural Science Foundation of ChinaNational Key Research and Development Program of ChinaKey Collaborative Research Program of the Alliance of International Science OrganizationsHaplotype networks are graphs used to represent evolutionary relationships between a set of taxa and are characterized by intuitiveness in analyzing genealogical relationships of closely related genomes. We here propose a novel algorithm termed McAN that considers mutation spectrum history (mutations in ancestry haplotype should be contained in descendant haplotype), node size (corresponding to sample count for a given node) and sampling time when constructing haplotype network. We show that McAN is two orders of magnitude faster than state-of-the-art algorithms without losing accuracy, making it suitable for analysis of a large number of sequences. Based on our algorithm, we developed an online web server and offline tool for haplotype network construction, community lineage determinationBriefings in bioinformaticsbbad174https://www.ebi.ac.uk/biostudies/studies/S-EPMC10199771biostudies-literatureMcAN: a novel computational algorithm and platform for constructing and visualizing haplotype networks.PMC101997713227071832170678Z21110000212100620171412021YFC0863300XDB38060100ANSO-CR-KP-2022-092021YFF0703703Shi LWang ALi CBao YZhao WTian DLi LLi NXue YZhu JZhang ZXu BSong SfalseMcAN: a novel computational algorithm and platform for constructing and visualizing haplotype networks.Haplotype networks are graphs used to represent evolutionary relationships between a set of taxa and are characterized by intuitiveness in analyzing genealogical relationships of closely related genomes. We here propose a novel algorithm termed McAN that considers mutation spectrum history (mutations in ancestry haplotype should be contained in descendant haplotype), node size (corresponding to sample count for a given node) and sampling time when constructing haplotype network. We show that McAN is two orders of magnitude faster than state-of-the-art algorithms without losing accuracy, making it suitable for analysis of a large number of sequences. Based on our algorithm, we developed an online web server and offline tool for haplotype network construction, community lineage determination2023-01-01T00:00:00Z2023 May2025-04-04T09:58:12.676Z2024-11-07T12:08:47.299ZS-EPMC101997713717075210.1093/bib/bbad174