TreeFam v9: a new website, more species and orthology-on-the-fly

Hieranoid: Hierarchical Orthology Inference

(2013) Fabian Schreiber et al.   JOURNAL OF MOLECULAR BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm

(2012) Ari Löytynoja et al.   BIOINFORMATICS

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2012)   NUCLEIC ACIDS RESEARCH

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

(2012) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

WormBase 2012: more genomes, more data, new website

(2011) K. Yook et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

(2010) J. Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

OMA 2011: orthology inference among 1000 complete genomes

(2010) A. M. Altenhoff et al.   NUCLEIC ACIDS RESEARCH

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Berkeley PHOG: PhyloFacts orthology group prediction web server

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

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

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