Computational phylogenetics

Research in Dr. McMahon's lab focuses on the analysis of biological diversity, particularly through phylogenetic systematics of plants. Lab-based work includes comparative molecular sequencing, aimed at inferring evolutionary relationships among lineages in the legume family (Fabaceae), and using the resulting phylogenies to infer historical rates and modes of floral morphological evolution. Computational research includes testing data from public molecular sequence databases for the ability to construct large-scale phylogenetic trees for all 1.7 million known species, investigating theoretical limits to phylogenetic inference, and developing software for analyzing the effects of fragmentation in phylogenetic and phylogenomic data sets

John Kececioglu is an Associate Professor in the Department of Computer Science, and the BIO5 Institute. His research is in applied algorithms, especially for areas of bioinformatics and computational biology such as: multiple alignment, inverse alignment, sequence assembly, and genome rearrangement. Software developed by his group includes Opal, a tool for multiple sequence alignment; Facet, a tool for alignment accuracy estimation; Ipa, a tool for inverse sequence alignment; AlignAlign, a tool for optimally aligning alignments, and Ninja, a tool for evolutionary tree construction. John is a recipient of a National Science Foundation CAREER Award, serves as an Associate Editor for IEEE/ACM Transactions on Computational Biology and Bioinformatics, and is on the Editorial Board of Algorithms for Molecular Biology. He was Conference Chair for RECOMB 2009, and Program Committee Co-Chair in the area of Sequence Analysis for ISMB 2011 and BCB 2012. John served as Associate Head of the Department of Computer Science during 2012.