Structure-aware models and algorithms for reconstructing the evolution and ancestral states of genes and genomes

这是一个计算基因组学研究计划，旨在解决算法和计算问题，以提高我们对基因组进化的理解。目前，大多数基因组进化重建方法仅限于使用基因组的序列保守部分，而很少关注组分的结构。然而，目前生命科学的发现正在揭示基因结构的复杂性及其对基因功能和进化的重要性。特别是非编码RNA（ncRNA）的二级结构和真核生物编码基因的结构构成了重建基因进化和祖先状态的有价值的信息。

This is a computational genomics research program aimed at solving algorithmic and computational problems in order to improve our understanding of genome evolution. Currently, most genome evolution reconstruction methods are limited to the use of sequence-conserved portions of genomes, paying less attention to the structure of components. However, current discoveries in the life sciences are shedding new light on the complexity of gene structure and its importance for gene function and evolution. In particular, the secondary structure of non-coding RNAs (ncRNAs) and the architecture of eukaryotic coding genes constitute valuable information for the reconstruction of gene evolution and ancestral states.