DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood

Birth, Death, and Diversification of Mobile Promoters in Prokaryotes

(2014) Mark W.J. van Passel et al.   GENETICS

Horizontal Transfer and Gene Conversion as an Important Driving Force in Shaping the Landscape of Mitochondrial Introns

(2014) Baojun Wu et al.   G3-Genes Genomes Genetics

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

Patterns of population epigenomic diversity

(2013) Robert J. Schmitz et al.   NATURE

BadiRate: estimating family turnover rates by likelihood-based methods

(2011) P. Librado et al.   BIOINFORMATICS

A Bayesian model for gene family evolution

(2011) Liang Liu et al.   BMC BIOINFORMATICS

GLOOME: gain loss mapping engine

(2010) O. Cohen et al.   BIOINFORMATICS

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

(2010) M. Csuos   BIOINFORMATICS

Inferring Bacterial Genome Flux While Considering Truncated Genes

(2010) Weilong Hao et al.   GENETICS

A Phylogenetic Mixture Model for Gene Family Loss in Parasitic Bacteria

(2009) Matthew Spencer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Uncovering rate variation of lateral gene transfer during bacterial genome evolution

(2008) Weilong Hao et al.   BMC GENOMICS

A likelihood framework to analyse phyletic patterns

(2008) O. Cohen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES