Phase determination from direct sequencing of length‐variable DNA regions

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The new systematics of scleractinia: Integrating molecular and morphological evidence (2016, background): “For regions that have not diverged considerably between paralogues, such as the ITS, mixed PCR products can be split into two dominant sequences based on phase reconstruction of forward and reverse chromatograms of distinct lengths (Flot and Tillier 2006; Flot et al. 2006).”
seqphase: a web tool for interconverting phase input/output files and fasta sequence alignments (2010, background): “Another issue concerns length-variant heterozygotes, i.e. individuals whose haplotypes are of different lengths because of the presence of one or several indels (Creer et al. 2005; Flot et al. 2006).”