SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction

Active site prediction using evolutionary and structural information

(2010) Sriram Sankararaman et al.   BIOINFORMATICS

Getting Started in Structural Phylogenomics

(2010) Kimmen Sjölander   PLoS Computational Biology

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

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

Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy

(2009) K. Liu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Berkeley PHOG: PhyloFacts orthology group prediction web server

(2009) Ruchira S. Datta et al.   NUCLEIC ACIDS RESEARCH

Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

(2009) K. Liu et al.   SCIENCE

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

(2009) John A. Capra et al.   PLoS Computational Biology

INTREPID—INformation-theoretic TREe traversal for Protein functional site IDentification

(2008) Sriram Sankararaman et al.   BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Large-scale assignment of orthology: back to phylogenetics?

(2008) Toni Gabaldón   GENOME BIOLOGY