TreeExp2: An Integrated Framework for Phylogenetic Transcriptome Analysis.
IF: 4.065
Cited by: 2


Recent innovations of next-generation sequencing such as RNA-seq have generated an enormous amount of comparative transcriptome data, which have shed lights on our understanding of the complexity of transcriptional regulatory systems. Despite numerous RNA-seq analyses, statistical methods and computational tools designed for phylogenetic transcriptome analysis and evolution have not been well developed. In response to this need, we developed software TreeExp2 specifically for RNA-seq data. The R-package TreeExp2 has implemented a suite of advanced, recently developed methods for transcriptome evolutionary analysis. Its main functions include the ancestral transcriptome inference, estimation of the strength of expression conservation, new expression distance, and the relative expression rate test. TreeExp2 provides an integrated, statistically sound framework for phylogenetic transcriptome analysis. It will considerably enhance our analytical capability for exploring the evolution and selection at the transcriptome level. The current version of TreeExp2 is available under GPLv3 license at the Github developer site; last accessed November 12, 2019, and its online tutorial which describes the biological theories in details and fully worked case studies with real data can be found at; last accessed November 12, 2019.


Gene Expression
high-throughput analysis
transcriptome evolution

MeSH terms

Computational Biology
Gene Expression Profiling
High-Throughput Nucleotide Sequencing
Sequence Analysis, RNA


Yang, Jingwen
Ruan, Hang
Xu, Wenjie
Gu, Xun

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