Related references
Note: Only part of the references are listed.Orthology prediction methods: A quality assessment using curated protein families
Kalliopi Trachana et al.
BIOESSAYS (2011)
OrthoInspector: comprehensive orthology analysis and visual exploration
Benjamin Linard et al.
BMC BIOINFORMATICS (2011)
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees
Brigitte Boeckmann et al.
BRIEFINGS IN BIOINFORMATICS (2011)
Computational methods for Gene Orthology inference
David M. Kristensen et al.
BRIEFINGS IN BIOINFORMATICS (2011)
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011
Robert M. Waterhouse et al.
NUCLEIC ACIDS RESEARCH (2011)
Ongoing and future developments at the Universal Protein Resource
Rolf Apweiler et al.
NUCLEIC ACIDS RESEARCH (2011)
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
Damian Szklarczyk et al.
NUCLEIC ACIDS RESEARCH (2011)
OMA 2011: orthology inference among 1000 complete genomes
Adrian M. Altenhoff et al.
NUCLEIC ACIDS RESEARCH (2011)
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
Ivica Letunic et al.
NUCLEIC ACIDS RESEARCH (2011)
Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer
Christopher J. Creevey et al.
PLOS ONE (2011)
STITCH 2: an interaction network database for small molecules and proteins
Michael Kuhn et al.
NUCLEIC ACIDS RESEARCH (2010)
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
J. Muller et al.
NUCLEIC ACIDS RESEARCH (2010)
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
Gabriel Ostlund et al.
NUCLEIC ACIDS RESEARCH (2010)
SIMAP-a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters
Thomas Rattei et al.
NUCLEIC ACIDS RESEARCH (2010)
2x genomes - depth does matter
Michel C. Milinkovitch et al.
GENOME BIOLOGY (2010)
Jalview Version 2-a multiple sequence alignment editor and analysis workbench
Andrew M. Waterhouse et al.
BIOINFORMATICS (2009)
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
Albert J. Vilella et al.
GENOME RESEARCH (2009)
SMART 6: recent updates and new developments
Ivica Letunic et al.
NUCLEIC ACIDS RESEARCH (2009)
Berkeley PHOG: PhyloFacts orthology group prediction web server
Ruchira S. Datta et al.
NUCLEIC ACIDS RESEARCH (2009)
ProGMap: an integrated annotation resource for protein orthology
Arnold Kuzniar et al.
NUCLEIC ACIDS RESEARCH (2009)
GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis
Cristina Aurrecoechea et al.
NUCLEIC ACIDS RESEARCH (2009)
Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods
Adrian M. Altenhoff et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
The quest for orthologs: finding the corresponding gene across genomes
Arnold Kuzniar et al.
TRENDS IN GENETICS (2008)
Large-scale assignment of orthology: back to phylogenetics?
Toni Gabaldon
GENOME BIOLOGY (2008)
The Arabidopsis Information Resource (TAIR): gene structure and function annotation
David Swarbreck et al.
NUCLEIC ACIDS RESEARCH (2008)
TreeFam: 2008 update
Jue Ruan et al.
NUCLEIC ACIDS RESEARCH (2008)
eggNOG: automated construction and annotation of orthologous groups of genes
Lars Juhl Jensen et al.
NUCLEIC ACIDS RESEARCH (2008)
PhylomeDB: a database for genome-wide collections of gene phylogenies
Jaime Huerta-Cepas et al.
NUCLEIC ACIDS RESEARCH (2008)
The Pfam protein families database
Robert D. Finn et al.
NUCLEIC ACIDS RESEARCH (2008)
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea
Kira S. Makarova et al.
BIOLOGY DIRECT (2007)
Automatic genome-wide reconstruction of phylogenetic gene trees
Ilan Wapinski et al.
BIOINFORMATICS (2007)
Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes
Feng Chen et al.
PLOS ONE (2007)
Orthology prediction at scalable resolution by phylogenetic tree analysis
Rene T. J. M. van der Heijden et al.
BMC BIOINFORMATICS (2007)
MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups
Ikuo Uchiyama
NUCLEIC ACIDS RESEARCH (2007)
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
Kim D. Pruitt et al.
NUCLEIC ACIDS RESEARCH (2007)
Toward automatic reconstruction of a highly resolved tree of life
FD Ciccarelli et al.
SCIENCE (2006)
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
Feng Chen et al.
NUCLEIC ACIDS RESEARCH (2006)
Benchmarking ortholog identification methods using functional genomics data
Tim Hulsen et al.
GENOME BIOLOGY (2006)
STRING: known and predicted protein-protein associations, integrated and transferred across organisms
C von Mering et al.
NUCLEIC ACIDS RESEARCH (2005)
The COG database: an updated version includes eukaryotes
RL Tatusov et al.
BMC BIOINFORMATICS (2003)
Function prediction and protein networks
MA Huynen et al.
CURRENT OPINION IN CELL BIOLOGY (2003)