AllelePipe is a pipeline to cluster putative alleles within and among individuals. AllelePipe is designed specifically for cases in which read depth information is not appropriate or available to assist with disentangling closely related paralogs from allelic variation, as in transcriptome or previously assembled libraries.
The Dlugosch Lab @ The University of Arizona
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G3 (Bethesda). 2013 Feb;3(2):359-67. doi: 10.1534/g3.112.003871.
Allele identification for transcriptome-based population genomics in the invasive plant Centaurea solstitialis.
Dlugosch KM, Lai Z, Bonin A, Hierro J, Rieseberg LH.