相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Endosymbiotic origin and differential loss of eukaryotic genes
Chuan Ku et al.
NATURE (2015)
Structure and function of the global ocean microbiome
Shinichi Sunagawa et al.
SCIENCE (2015)
OrthoInspector 2.0: Software and database updates
Benjamin Linard et al.
BIOINFORMATICS (2015)
Expanded microbial genome coverage and improved protein family annotation in the COG database
Michael Y. Galperin et al.
NUCLEIC ACIDS RESEARCH (2015)
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software
Evgenia V. Kriventseva et al.
NUCLEIC ACIDS RESEARCH (2015)
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements
Adrian M. Altenhoff et al.
NUCLEIC ACIDS RESEARCH (2015)
Gene Ontology Consortium: going forward
J. A. Blake et al.
NUCLEIC ACIDS RESEARCH (2015)
SMART: recent updates, new developments and status in 2015
Ivica Letunic et al.
NUCLEIC ACIDS RESEARCH (2015)
Ensembl 2015
Fiona Cunningham et al.
NUCLEIC ACIDS RESEARCH (2015)
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
Erik L. L. Sonnhammer et al.
NUCLEIC ACIDS RESEARCH (2015)
STRING v10: protein-protein interaction networks, integrated over the tree of life
Damian Szklarczyk et al.
NUCLEIC ACIDS RESEARCH (2015)
UniProt: a hub for protein information
Alex Bateman et al.
NUCLEIC ACIDS RESEARCH (2015)
An integrated catalog of reference genes in the human gut microbiome
Junhua Li et al.
NATURE BIOTECHNOLOGY (2014)
SIMAP-the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage
Roland Arnold et al.
NUCLEIC ACIDS RESEARCH (2014)
eggNOG v4.0: nested orthology inference across 3686 organisms
Sean Powell et al.
NUCLEIC ACIDS RESEARCH (2014)
Ensembl Genomes 2013: scaling up access to genome-wide data
Paul Julian Kersey et al.
NUCLEIC ACIDS RESEARCH (2014)
RefSeq microbial genomes database: new representation and annotation strategy
Tatiana Tatusova et al.
NUCLEIC ACIDS RESEARCH (2014)
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome
Jaime Huerta-Cepas et al.
NUCLEIC ACIDS RESEARCH (2014)
The genome portal of the Department of Energy Joint Genome Institute: 2014 updates
Henrik Nordberg et al.
NUCLEIC ACIDS RESEARCH (2014)
Pfam: the protein families database
Robert D. Finn et al.
NUCLEIC ACIDS RESEARCH (2014)
Data, information, knowledge and principle: back to metabolism in KEGG
Minoru Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2014)
STITCH 4: integration of protein-chemical interactions with user data
Michael Kuhn et al.
NUCLEIC ACIDS RESEARCH (2014)
A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation
Kalliopi Trachana et al.
PLOS ONE (2014)
Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes
David M. Kristensen et al.
JOURNAL OF BACTERIOLOGY (2013)
Hieranoid: Hierarchical Orthology Inference
Fabian Schreiber et al.
JOURNAL OF MOLECULAR BIOLOGY (2013)
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh et al.
MOLECULAR BIOLOGY AND EVOLUTION (2013)
Functional and evolutionary implications of gene orthology
Toni Gabaldon et al.
NATURE REVIEWS GENETICS (2013)
Following Gene Duplication, Paralog Interference Constrains Transcriptional Circuit Evolution
Christopher R. Baker et al.
SCIENCE (2013)
Orthology prediction methods: A quality assessment using curated protein families
Kalliopi Trachana et al.
BIOESSAYS (2011)
Assigning duplication events to relative temporal scales in genome-wide studies
Jaime Huerta-Cepas et al.
BIOINFORMATICS (2011)
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
Fabian Sievers et al.
MOLECULAR SYSTEMS BIOLOGY (2011)
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score
Leszek P. Pryszcz et al.
NUCLEIC ACIDS RESEARCH (2011)
Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals
Nathan L. Nehrt et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
Accelerated Profile HMM Searches
Sean R. Eddy
PLOS COMPUTATIONAL BIOLOGY (2011)
ETE: a python Environment for Tree Exploration
Jaime Huerta-Cepas et al.
BMC BIOINFORMATICS (2010)
FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments
Morgan N. Price et al.
PLOS ONE (2010)
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
Stephane Guindon et al.
SYSTEMATIC BIOLOGY (2010)
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Salvador Capella-Gutierrez et al.
BIOINFORMATICS (2009)
How confident can we be that orthologs are similar, but paralogs differ?
Romain A. Studer et al.
TRENDS IN GENETICS (2009)
eggNOG: automated construction and annotation of orthologous groups of genes
Lars Juhl Jensen et al.
NUCLEIC ACIDS RESEARCH (2008)
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways
Huaiyu Mi et al.
NUCLEIC ACIDS RESEARCH (2007)
Bushes in the tree of life
Antonis Rokas et al.
PLOS BIOLOGY (2006)
Toward automatic reconstruction of a highly resolved tree of life
FD Ciccarelli et al.
SCIENCE (2006)
M-Coffee: combining multiple sequence alignment methods with T-Coffee
IM Wallace et al.
NUCLEIC ACIDS RESEARCH (2006)
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
Feng Chen et al.
NUCLEIC ACIDS RESEARCH (2006)
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
RC Edgar
BMC BIOINFORMATICS (2004)
The COG database: an updated version includes eukaryotes
RL Tatusov et al.
BMC BIOINFORMATICS (2003)