Ortholog identification in the presence of domain architecture rearrangement

Active site prediction using evolutionary and structural information

(2010) Sriram Sankararaman et al.   BIOINFORMATICS

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes

(2010) Amrita Pati et al.   NATURE METHODS

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

(2010) R. Hagopian et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Getting Started in Structural Phylogenomics

(2010) Kimmen Sjölander   PLoS Computational Biology

Berkeley PHOG: PhyloFacts orthology group prediction web server

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

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

Joining forces in the quest for orthologs

(2009) Toni Gabaldón et al.   GENOME BIOLOGY

Recent developments in the MAFFT multiple sequence alignment program

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

Evolution of protein domain promiscuity in eukaryotes

(2008) M. K. Basu et al.   GENOME RESEARCH

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Domain-Based and Family-Specific Sequence Identity Thresholds Increase the Levels of Reliable Protein Function Transfer

(2008) Sarah Addou et al.   JOURNAL OF MOLECULAR BIOLOGY

The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies

(2008) A. L. Cuff et al.   NUCLEIC ACIDS RESEARCH

Taxon Sampling Affects Inferences of Macroevolutionary Processes from Phylogenetic Trees

(2008) Tracy A. Heath et al.   SYSTEMATIC BIOLOGY

The quest for orthologs: finding the corresponding gene across genomes

(2008) Arnold Kuzniar et al.   TRENDS IN GENETICS