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Allopolyploidy analysis software tools | RNA sequencing data

Forming a new species through the merger of two or more divergent parent species is increasingly seen as a key phenomenon in the evolution of many biological systems. However, little is known about how expression of parental gene copies (homeologs)…
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HomeoRoq
Desktop

HomeoRoq Homeolog Ratio and Quantification

Quantifies the contribution of gene expression of each homeolog. HomeoRoq can…

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…

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HyLiTE
Desktop

HyLiTE Hybrid Lineage Transcriptome Explorer

Analyzes high-throughput transcriptome data from allopolyploid species. HyLiTE…

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…

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HomeoSplitter
Desktop

HomeoSplitter

A fast and effective solution to disentangle homeologous sequences based on a…

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…

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SNiPloid
Web

SNiPloid

A software tool that exploits and interprets putative SNPs in the context of…

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…

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PolyCat
Desktop

PolyCat

A pipeline for mapping and categorizing all types of next-generation sequence…

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…

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