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Genome Biology and Evolution|October 6, 2011
Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony--a simulation studyOfir Cohen, Tal PupkoBioinformatics (Oxford, England)|December 28, 2018
Ancestral sequence reconstruction: accounting for structural information by averaging over replacement matricesAsher Moshe, Tal PupkoProceedings. Biological Sciences|June 25, 2002
A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomesTal Pupko, Nicolas GaltierMolecular Biology and Evolution|October 8, 2009
Inference and characterization of horizontally transferred gene families using stochastic mappingOfir Cohen, Tal PupkoMolecular Biology and Evolution|November 18, 2006
A combined empirical and mechanistic codon modelAdi Doron-Faigenboim, Tal PupkoMolecular Biology and Evolution|December 15, 2010
The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transferOfir Cohen, Uri Gophna, Tal PupkoBioinformatics (Oxford, England)|October 6, 2005
A gamma mixture model better accounts for among site rate heterogeneityItay Mayrose, Nir Friedman, Tal PupkoMolecular Biology and Evolution|July 21, 2011
Improving the performance of positive selection inference by filtering unreliable alignment regionsEyal Privman, Osnat Penn, Tal PupkoJournal of Molecular Evolution|May 5, 2005
Site-specific evolutionary rate inference: taking phylogenetic uncertainty into accountItay Mayrose, Amir Mitchell, Tal PupkoBMC Evolutionary Biology|March 15, 2006
Paths of lateral gene transfer of lysyl-aminoacyl-tRNA synthetases with a unique evolutionary transition stage of prokaryotes coding for class I and II varieties by the same organismsShaul Shaul, Ruth Nussinov, Tal PupkoPageof 19