PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

State-of the art methodologies dictate new standards for phylogenetic analysis

(2013) Maria Anisimova et al.   BMC EVOLUTIONARY BIOLOGY

Comparative transcriptomics of early dipteran development

(2013) Eva Jiménez-Guri et al.   BMC GENOMICS

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification

(2013) Cyrus Afrasiabi et al.   NUCLEIC ACIDS RESEARCH

Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida

(2013) J. Collen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward community standards in the quest for orthologs

(2012) C. Dessimoz et al.   BIOINFORMATICS

The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite’s biology

(2012) Larissa Silva et al.   BMC GENOMICS

Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus

(2012) Marina Marcet-Houben et al.   BMC GENOMICS

FlyBase: improvements to the bibliography

(2012) Steven J. Marygold 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

The genome of melon (Cucumis melo L.)

(2012) J. Garcia-Mas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

(2011) B. Boeckmann et al.   BRIEFINGS IN BIOINFORMATICS

Letter to the Editor: SeqXML and OrthoXML: standards for sequence and orthology information

(2011) T. Schmitt et al.   BRIEFINGS IN BIOINFORMATICS

The Génolevures database

(2011) Tiphaine Martin et al.   COMPTES RENDUS BIOLOGIES

The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata

(2011) D. O. Inglis et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

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

Assigning duplication events to relative temporal scales in genome-wide studies

(2010) J. Huerta-Cepas et al.   BIOINFORMATICS

ETE: a python Environment for Tree Exploration

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

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

MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score

(2010) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

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

2× genomes - depth does matter

(2010) Michel C Milinkovitch et al.   GENOME BIOLOGY

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

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

Databases of homologous gene families for comparative genomics

(2009) Simon Penel et al.   BMC BIOINFORMATICS

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

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

(2009) Adrian M. Altenhoff et al.   PLoS Computational Biology

Joining forces in the quest for orthologs

(2009) Toni Gabaldón et al.   GENOME BIOLOGY

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

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

The GOA database in 2009--an integrated Gene Ontology Annotation resource

(2008) D. Barrell et al.   NUCLEIC ACIDS RESEARCH

Large-scale assignment of orthology: back to phylogenetics?

(2008) Toni Gabaldón   GENOME BIOLOGY