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

Author:

Vences Miguel1ORCID,Patmanidis Stefanos2,Schmidt Jan-Christopher1,Matschiner Michael3,Miralles Aurélien14,Renner Susanne S5ORCID

Affiliation:

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

2. Department of Computer Science, School of Electrical and Computer Engineering, National Technical University of Athens , 15780 Athens, Greece

3. Natural History Museum, University of Oslo , 0562 Oslo, Norway

4. Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE , 75005 Paris, France

5. Department of Biology, Washington University , Saint Louis, MO 63130, United States

Abstract

Abstract Motivation Haplotype networks are a routine approach to visualize relationships among alleles. Such visual analysis of single-locus data is still of importance, especially in species diagnosis and delimitation, where a limited amount of sequence data usually are available and sufficient, along with other datasets in the framework of integrative taxonomy. In diploid organisms, this often requires separating (phasing) sequences with heterozygotic positions, and typically separate programs are required for phasing, reformatting of input files, and haplotype network construction. We therefore developed Hapsolutely, a user-friendly program with an ergonomic graphical user interface that integrates haplotype phasing from single-locus sequences with five approaches for network/genealogy reconstruction. Results Among the novel options implemented, Hapsolutely integrates phasing and graphical reconstruction steps of haplotype networks, supports input of species partition data in the common SPART and SPART-XML formats, and calculates and visualizes haplowebs and fields for recombination, thus allowing graphical comparison of allele distribution and allele sharing among subsets for the purpose of species delimitation. The new tool has been specifically developed with a focus on the workflow in alpha-taxonomy, where exploring fields for recombination across alternative species partitions may help species delimitation. Availability and implementation Hapsolutely is written in Python, and integrates code from Phase, SeqPHASE, and PopART in C++ and Haxe. Compiled stand-alone executables for MS Windows and Mac OS along with a detailed manual can be downloaded from https://www.itaxotools.org; the source code is openly available on GitHub (https://github.com/iTaxoTools/Hapsolutely).

Funder

Deutsche Forschungsgemeinschaft

Publisher

Oxford University Press (OUP)

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