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. 2013 Feb 1;3(2):359–367. doi: 10.1534/g3.112.003871

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Copyright © 2013 Dlugosch et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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AllelePipe workflow for identifying alleles without a reference genome. Unigenes from all individuals are pooled and clustered by similarity. Clustered sequences are aligned and consensus sequences are generated, providing a pseudo-reference genome. Unigenes from the same and/or different individuals are aligned to the reference, and SNPs are identified. Multilocus SNP information is used to construct a minimum set of haplotypes for each individual, and clusters in which individuals are represented by an excess number of putative alleles are flagged as potential multigene clusters.