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

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

DeathBase: a database on structure, evolution and function of proteins involved in apoptosis and other forms of cell death

(2010) J Díez et al.   CELL DEATH AND DIFFERENTIATION

The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes

(2010) J. Huerta-Cepas et al.   INSECT MOLECULAR BIOLOGY

Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains

(2010) Arantxa Peña et al.   ISME Journal

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

(2010)   PLOS BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

(2009) J. Muller et al.   NUCLEIC ACIDS RESEARCH

PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome

(2009) Agatha Schlüter et al.   NUCLEIC ACIDS RESEARCH

The Universal Protein Resource (UniProt) in 2010

(2009)   NUCLEIC ACIDS RESEARCH

The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome

(2009) Marina Marcet-Houben et al.   PLoS One

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

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

The quest for orthologs: finding the corresponding gene across genomes

(2008) Arnold Kuzniar et al.   TRENDS IN GENETICS

Large-scale assignment of orthology: back to phylogenetics?

(2008) Toni Gabaldón   GENOME BIOLOGY