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Hapsolutely: a user-friendly tool integrating haplotype phasing, network construction, and haploweb calculation.

Miguel Vences1, Stefanos Patmanidis2, Jan-Christopher Schmidt1

  • 1Division of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany.

Bioinformatics Advances
|June 19, 2024
PubMed
Summary

Hapsolutely is a new, user-friendly program that integrates haplotype phasing and network reconstruction for species delimitation. This tool simplifies complex analyses, aiding in alpha-taxonomy and species diagnosis with limited sequence data.

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Area of Science:

  • Genetics
  • Bioinformatics
  • Taxonomy

Background:

  • Haplotype networks visualize allele relationships, crucial for species diagnosis and delimitation.
  • Analyzing single-locus data in diploid organisms often requires complex phasing and data reformatting steps.
  • Existing workflows typically necessitate separate programs for phasing, file reformatting, and network construction.

Purpose of the Study:

  • To develop a user-friendly program integrating haplotype phasing and network reconstruction.
  • To streamline the process of analyzing single-locus sequence data for species delimitation.
  • To provide a tool that aids researchers in alpha-taxonomy and species diagnosis.

Main Methods:

  • Developed Hapsolutely, a program with a graphical user interface.
  • Integrated haplotype phasing from single-locus sequences.
  • Incorporated five approaches for network/genealogy reconstruction.

Main Results:

  • Hapsolutely integrates phasing and graphical reconstruction of haplotype networks.
  • Supports SPART and SPART-XML formats for species partition data.
  • Calculates and visualizes haplowebs and recombination fields for species delimitation.

Conclusions:

  • Hapsolutely simplifies the analysis of haplotype data for species delimitation.
  • The tool facilitates graphical comparison of allele distribution and sharing among subsets.
  • It is particularly useful for alpha-taxonomy workflows involving species partitioning.