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

MotivationThe simultaneous consideration of sequence alignment and RNA secondary structure, or structural alignment, is known to help predict more accurate secondary structures of homologs. However, the consideration is heavy and can be done only roughly to decompose structural alignments. ResultsThe PhyloFold method, which predicts secondary structures of homologs considering likely pairwise structural alignments, was developed in this study. The method shows the best prediction accuracy while demanding comparable running time compared to conventional methods. AvailabilityThe 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". Supplementary informationSupplementary data are available.