TREND is a platform that allows researchers to explore protein function identifying protein features, gene neighborhoods and operons, clustering neighboring genes, and integrating all these data into phylogenomic context and cross-referencing with RefSeq, Pfam, CDD and MiST databases. The platform provides ample opportunities for adjusting each step of the analysis.
TREND has an extensible modular architecture, new functionality can be added with little effort. The backbone of the platform is written in Java, new modules can be written in any language and integrated in the platform as long as they can be launched as command-line applications controlled by parameters.
TREND stands for TRee-based Exploration of Neighborhoods and Domains.
Vadim M. Gumerov, Igor B. Zhulin (2020). TREND: a platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses. Nucleic Acids Research, gkaa243, https://doi.org/10.1093/nar/gkaa243