HiMAP2: Identifying phylogenetically informative genetic markers from diverse genomic resources

Oksana V. Vernygora, Carlos Congrains, Scott M. Geib, Julian R. Dupuis

Research output: Contribution to journalArticlepeer-review


Multiplexed amplicon sequencing offers a cost-effective and rapid solution for phylogenomic studies that include a large number of individuals. Selecting informative genetic markers is a critical initial step in designing such multiplexed amplicon panels, but screening various genomic data and selecting markers that are informative for the question at hand can be laborious. Here, we present a flexible and user-friendly tool, HiMAP2, for identifying, visualizing and filtering phylogenetically informative loci from diverse genomic and transcriptomic resources. This bioinformatics pipeline includes orthology prediction, exon extraction and filtering of aligned exon sequences according to user-defined specifications. Additionally, HiMAP2 facilitates exploration of the final filtered exons by incorporating phylogenetic inference of individual exon trees with raxml-ng as well as the estimation of a species tree using astral. Finally, results of the marker selection can be visualized and refined with an interactive Bokeh application that can be used to generate publication-quality figures. Source code and user instructions for HiMAP2 are available at https://github.com/popphylotools/HiMAP_v2.

Original languageEnglish
Pages (from-to)1155-1167
Number of pages13
JournalMolecular Ecology Resources
Issue number5
StatePublished - Jul 2023

Bibliographical note

Publisher Copyright:
© 2023 John Wiley & Sons Ltd.


  • comparative genomics
  • genome
  • phylogenetic informativeness
  • targeted amplicon design
  • transcriptome

ASJC Scopus subject areas

  • Biotechnology
  • Ecology, Evolution, Behavior and Systematics
  • Genetics


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