Quantifies the contribution of gene expression of each homeolog. HomeoRoq can detect changes in the ratios of the expression of homeologs under different conditions using RNA-seq data obtained from synthetic allopolyploid species. The software works with draft genomes or gene sequences assembled using a RNA-seq assembler. It does not need prior single nucleotide polymorphism (SNP) analysis between parental species.

A fast and effective solution to disentangle homeologous sequences based on a maximum likelihood optimization. HomeoSplitter provides a practical solution to the complex problem of disentangling homeologous transcripts in allo-tetraploids, which further allows an improved SNP detection.

Analyzes high-throughput transcriptome data from allopolyploid species. HyLiTE offers practical advantages over manual methods and existing programs, has been designed to accommodate a wide range of genome merger systems, can identify SNPs that arose following genome merger, and offers accurate performance on non-model organisms.

A pipeline for mapping and categorizing all types of next-generation sequence data produced from allopolyploid organisms. PolyCat uses GSNAP's single-nucleotide polymorphism (SNP)-tolerant mapping to minimize the mapping efficiency bias caused by SNPs between genomes. PolyCat then uses SNPs between genomes to categorize reads according to their respective genomes. PolyCat is appropriate for all allopolyploids and all types of next-generation genome analysis, including differential expression (RNA sequencing), differential methylation (bisulfite sequencing), differential DNA-protein binding (chromatin immunoprecipitation sequencing), and population diversity.

A software tool 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.