Indel evolution

Mechanisms, character coding, model development; indel evolution in chloroplast genomes

With the growing number of phylogenetic studies that use length variable DNA sequences, incorporating information from length-mutational events into phylogenetic analysis is becoming increasingly important. We work on indel coding methods that aim at maximizing the phylogenetic information retained from unambiguously aligned sequence regions or regions where the principal relative position of gaps to one another can be safely established. In cooperation with Prof. Simmons (Colorado State University, USA), we have compared previously published indel coding approaches to one another based on simulations and now continue with meta-analyses of empirical data. Our most recent collaborative work is on the reciprocal illumination of secondary structure prediction, alignment process, and hypothesized indel events.