Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss?

Phylogenomic clustering for selecting non-redundant genomes for comparative genomics

(2013) G. Moreno-Hagelsieb et al.   BIOINFORMATICS

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

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

RefSeq microbial genomes database: new representation and annotation strategy

(2013) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

Improving Microbial Genome Annotations in an Integrated Database Context

(2013) I-Min A. Chen et al.   PLoS One

Toward community standards in the quest for orthologs

(2012) C. Dessimoz et al.   BIOINFORMATICS

KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters

(2012) Akihiro Nakaya et al.   NUCLEIC ACIDS RESEARCH

OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis

(2012) Matthew D. Whiteside et al.   NUCLEIC ACIDS RESEARCH

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

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

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

(2012) Paul D. Thomas et al.   PLoS Computational Biology

The Ortholog Conjecture Is Untestable by the Current Gene Ontology but Is Supported by RNA Sequencing Data

(2012) Xiaoshu Chen et al.   PLoS Computational Biology

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

(2012) Adrian M. Altenhoff et al.   PLoS Computational Biology

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

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

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