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Background  Phylogenetic profiling is widely used to predict novel members of large protein complexes and biological pathways. Although methods combined with phylogenetic trees have significantly improved prediction accuracy, computational efficiency is still an issue that limits its genome-wise application.    Results  Here we introduce a new tree-based phylogenetic profiling algorithm named GFICLEE, which infers common single and continuous loss (SCL) events in the evolutionary patterns. We validated our algorithm with human pathways from three databases and compared the computational efficiency with current tree-based with 10 different scales genome dataset. Our algorithm has a better predictive performance with high computational efficiency.    Conclusions  The GFICLEE is a new method to infers genome-wide gene function. The accuracy and computational efficiency of GFICLEE make it possible to explore gene functions at the genome-wide level on a personal computer.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-08070-7.

GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level