MOABS

for comparing DNA methylation analysis between experimentswith D. Sun, Y. Xi, B. Rodriguez, T. Pan, M. Jeong, MA Goodell, W. Li, 2014

CPAT

for estimating coding potential of transcripts with L. Wang, S. Wang, J-P Kocher, W. Li, 2013

MURPAR

for inferring a phylogenetic network from a collection of gene trees with L. Nakhleh, 2012

NEPAL

for phylogenetic network construction using the maximum parsimony and maximum likelihood criteria with G. Jin and L. Nakhleh, 2010

SLS

for phylogenetic tree search under the maximum parsimony criterion with T. Williams, 2006