Hapsolutely

Hapsolutely integrates haplotype phasing, network construction, and haploweb calculation for integrative taxonomy workflows including species delimitation.

Key Features:

• Haplotype Phasing: Hapsolutely phases single-locus sequences with heterozygotic positions from diploid organisms.
• Network Reconstruction: Hapsolutely implements five approaches for network and genealogy reconstruction.
• Species Partition Input: Hapsolutely supports input of species partition data in SPART and SPART-XML formats.
• Haploweb Calculation and Visualization: Hapsolutely calculates and visualizes haplowebs and fields for recombination, enabling graphical comparison of allele distribution and allele sharing among subsets.
• Integrative Taxonomy Workflow: Hapsolutely combines data input, phasing, network reconstruction, and visualization steps for alpha-taxonomy applications.

Scientific Applications:

• Species Delimitation: Hapsolutely facilitates species diagnosis and delimitation by exploring fields for recombination across alternative species partitions.
• Allele Relationship Visualization: Hapsolutely visualizes relationships among alleles through haplotype network analysis of single-locus data.
• Integrative Taxonomy: Hapsolutely supports integrative taxonomy workflows where sequence data are combined with other datasets for species delimitation.

Methodology:

Hapsolutely integrates code from Phase, SeqPHASE, and PopART in C++ and Haxe, and is written in Python.