HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets.

Premise: Hybrids contain divergent alleles that can confound phylogenetic analyses but can provide insights into reticulated evolution when identified and phased. We developed a workflow to detect hybrids in target capture data sets and phase reads into parental lineages using a similarity and phylogenetic framework.

Methods: We used Angiosperms353 target capture data for , including known hybrids to test the novel workflow.