We develop methods that improve the accuracy of predicted protein function by using a phylogenomic approach integrating evolutionary tree construction and analysis in the annotation pipeline.

PhyloFacts – phylogenomic encyclopedias of protein families across the Tree of Life – More...

PHOG – PhyloFacts Orthology Group: phylogenetic orthologs – More...

PHOG PPI – Orthology-based protein-protein interaction prediction using the PHOG algorithm

INTREPID – INformation-theoretic TREe traversal for Protein functional site IDentification – More...

PhyloBuilder – build-your-own protein family tree – More...

FlowerPower – subfamily HMM clustering of homologs – More...

SCI-PHY – Subfamily Classification In PHYlogenomics: functional subfamily identification – More...

SATCHMO – Simultaneous Alignment and Tree Construction using Hidden Markov mOdels – More...