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.
Stöver BC, Müller KF: AlignmentComparator - Comparing and annotating alternative alignments of the same data set. IPAM Multiple Sequence Alignment Workshop; Los Angeles, USA; 2015 (Details)
Stöver BC, Müller KF: AlignmentComparator - A GUI application to efficiently visualize and annotate differences between alternative multiple sequence alignments. 4th annual Münster Graduate School of Evolution Symposium; Münster, Germany; 2014 (Details)
- AlignmentComparator (http://bioinfweb.info/AlignmentComparator)