FastML: a web server for probabilistic reconstruction of ancestral sequences

Utilizing natural diversity to evolve protein function: applications towards thermostability

(2011) Megan F Cole et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Inference of Gain and Loss Events from Phyletic Patterns Using Stochastic Mapping and Maximum Parsimony—A Simulation Study

(2011) Ofir Cohen et al.   Genome Biology and Evolution

maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences

(2010) Peter Menzel et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

A likelihood framework to analyse phyletic patterns

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

Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes

(2008) Osnat Penn et al.   PLoS Computational Biology