- HAL: a hierarchical format for storing and analyzing multiple genome alignmentsGlenn Hickey
Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz CA 95064, USA
Bioinformatics 29:1341-2. 2013..This loss of information grows with the number of species under comparison, as well as their phylogenetic distance...
- A probabilistic model for sequence alignment with context-sensitive indelsGlenn Hickey
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
J Comput Biol 18:1449-64. 2011..Fine-grained studies of small functional regions or disease markers, for example, could be significantly improved by our method. The implementation is available at www.mcb.mcgill.ca/~blanchem/software.html...
- A unifying model of genome evolution under parsimonyBenedict Paten
University of California, Santa Cruz, 1156 High St, 95064 Santa Cruz, USA
BMC Bioinformatics 15:206. 2014..Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation...