Alignment of single-cell trajectory trees with CAPITAL

Global alignment of complex pseudotime trajectories between different single-cell RNA-seq datasets is challenging, as existing tools mainly focus on linear alignment of single-cell trajectories. Here we present CAPITAL (comparative analysis of pseudotime trajectory inference with tree alignment), a method for comparing single-cell trajectories with tree alignment whereby branching trajectories can be automatically compared. Computational tests on synthetic datasets and authentic bone marrow cells datasets indicate that CAPITAL has achieved accurate and robust alignments of trajectory trees, revealing various gene expression dynamics including gene–gene correlation conservation between different species. Global alignment of complex cell state trajectories between single-cell datasets remains challenging. Here, the authors present a computational method called CAPITAL to compare branching trajectories, and demonstrate that this method achieves accurate and robust alignments.