SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species

High-throughput sequencing is a common approach to discover {SNP} variants, especially in plant species. However, methods to analyze predicted {SNPs} are often optimized for diploid plant species whereas many crop species are allopolyploids and combine related but divergent subgenomes (homoeologous chromosome sets). We created a software tool, {SNiPloid}, that exploits and interprets putative {SNPs} in the context of allopolyploidy by comparing {SNPs} from an allopolyploid with those obtained in its modern-day diploid progenitors. {SNiPloid} can compare {SNPs} obtained from a sample to estimate the subgenome contribution to the transcriptome or {SNPs} obtained from two polyploid accessions to search for {SNP} divergence.