From Gene Trees to Species Trees through a Supertree Approach Scornavacca Celine, Berry Vincent, Ranwez Vincent. 2009, Language and Automata Theory and Applications. 10.1007/978-3-642-00982-2_60
Fast NJ-like algorithms to deal with incomplete distance matrices Criscuolo Alexis, Gascuel Olivier. 2008, BMC Bioinformatics. 10.1186/1471-2105-9-166
Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics Is Clearly Beneficial Le Si Quang, Gascuel Olivier. 2010, Systematic Biology. 10.1093/sysbio/syq002
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data Gascuel O.. 1997, Molecular Biology and Evolution. 10.1093/oxfordjournals.molbev.a025808
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood Guindon Stéphane, Gascuel Olivier. 2003, Systematic Biology. 10.1080/10635150390235520
PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference Guindon S., Lethiec F., Duroux P., Gascuel O.. 2005, Nucleic Acids Research. 10.1093/nar/gki352
Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood Hordijk W., Gascuel O.. 2005, Bioinformatics. 10.1093/bioinformatics/bti713
Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative Anisimova Maria, Gascuel Olivier. 2006, Systematic Biology. 10.1080/10635150600755453
PhySIC: A Veto Supertree Method with Desirable Properties Ranwez Vincent, Berry Vincent, Criscuolo Alexis, Fabre Pierre-Henri, Guillemot Sylvain, Scornavacca Celine, Douzery Emmanuel J. P.. 2007, Systematic Biology. 10.1080/10635150701639754
An Improved General Amino Acid Replacement Matrix Le S. Q., Gascuel O.. 2008, Molecular Biology and Evolution. 10.1093/molbev/msn067
Phylogenetic mixture models for proteins Le Si Quang, Lartillot Nicolas, Gascuel Olivier. 2008, Philosophical Transactions of the Royal Society B: Biological Sciences. 10.1098/rstb.2008.0180
PhySIC_IST: cleaning source trees to infer more informative supertrees Scornavacca Celine, Berry Vincent, Lefort Vincent, Douzery Emmanuel JP, Ranwez Vincent. 2008, BMC Bioinformatics. 10.1186/1471-2105-9-413
SDM: A Fast Distance-Based Approach for (Super)Tree Building in Phylogenomics Criscuolo Alexis, Berry Vincent, Douzery Emmanuel J. P., Gascuel Olivier. 2006, Systematic Biology. 10.1080/10635150600969872
Phylogeny.fr: robust phylogenetic analysis for the non-specialist Dereeper A., Guignon V., Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J.-F., Guindon S., Lefort V., Lescot M., Claverie J.-M., Gascuel O.. 2008, Nucleic Acids Research. 10.1093/nar/gkn180
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 Guindon Stéphane, Dufayard Jean-François, Lefort Vincent, Anisimova Maria, Hordijk Wim, Gascuel Olivier. 2010, Systematic Biology. 10.1093/sysbio/syq010