PhyloFold: Precise and Swift Prediction of RNA Secondary Structures to Incorporate Phylogeny among Homologs

Motivation: The simultaneous consideration of sequence alignment and RNA secondary structure, structural alignment, has been known to help predict more accurate secondary structures of homologs. However, the consideration is heavy and has been done roughly to decompose structural alignments. Results: The PhyloFold method, which predicts secondary structures of homologs considering likely pairwise structual alignments between the homologs, is invented in this study. The method shows the best prediction accuracy while demanding comparable running time compared with competitors. Availability: The source code of the programs implemented in this study is available on "https://github.com/heartsh/phylofold" and "https://github.com/heartsh/phyloalifold". Contact: "tagashira_masaki_17@stu-cbms.k.u-tokyo.ac.jp".