Related references
Note: Only part of the references are listed.TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations
Haiming Tang et al.
BIOINFORMATICS (2019)
Rapid alignment-free phylogenetic identification of metagenomic sequences
Benjamin Linard et al.
BIOINFORMATICS (2019)
Advances and Applications in the Quest for Orthologs
Natasha Glover et al.
MOLECULAR BIOLOGY AND EVOLUTION (2019)
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold
Martin Steinegger et al.
NATURE METHODS (2019)
Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions
Rei Kajitani et al.
NATURE COMMUNICATIONS (2019)
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools
Huaiyu Mi et al.
NUCLEIC ACIDS RESEARCH (2019)
UniProt: a worldwide hub of protein knowledge
Alex Bateman et al.
NUCLEIC ACIDS RESEARCH (2019)
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
Jaime Huerta-Cepas et al.
NUCLEIC ACIDS RESEARCH (2019)
OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs
Evgenia V. Kriventseva et al.
NUCLEIC ACIDS RESEARCH (2019)
The Pfam protein families database in 2019
Sara El-Gebali et al.
NUCLEIC ACIDS RESEARCH (2019)
Benchmarking of alignment-free sequence comparison methods
Andrzej Zielezinski et al.
GENOME BIOLOGY (2019)
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
Jaime Huerta-Cepas et al.
MOLECULAR BIOLOGY AND EVOLUTION (2017)
Alignment-free sequence comparison: benefits, applications, and tools
Andrzej Zielezinski et al.
GENOME BIOLOGY (2017)
HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly
Shengfeng Huang et al.
BIOINFORMATICS (2017)
HIPPI: highly accurate protein family classification with ensembles of HMMs
Nam-phuong Nguyen et al.
BMC GENOMICS (2016)
The phylogeny, evolutionary developmental biology, and paleobiology of the Deuterostomia: 25 years of new techniques, new discoveries, and new ideas
Kevin J. Peterson et al.
ORGANISMS DIVERSITY & EVOLUTION (2016)
Spaced seeds improve k-mer-based metagenomic classification
Karel Brinda et al.
BIOINFORMATICS (2015)
The Genome 10K Project: A Way Forward
Klaus-Peter Koepfli et al.
ANNUAL REVIEW OF ANIMAL BIOSCIENCES, VOL 3 (2015)
Fast and sensitive protein alignment using DIAMOND
Benjamin Buchfink et al.
NATURE METHODS (2015)
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
Erik L. L. Sonnhammer et al.
NUCLEIC ACIDS RESEARCH (2015)
SCOPe: Structural Classification of Proteins-extended, integrating SCOP and ASTRAL data and classification of new structures
Naomi K. Fox et al.
NUCLEIC ACIDS RESEARCH (2014)
TreeFam v9: a new website, more species and orthology-on-the-fly
Fabian Schreiber et al.
NUCLEIC ACIDS RESEARCH (2014)
Kraken: ultrafast metagenomic sequence classification using exact alignments
Derrick E. Wood et al.
GENOME BIOLOGY (2014)
The i5K Initiative:Advancing Arthropod Genomics for Knowledge, Human Health,Agriculture, and the Environment i5K CONSORTIUM
Jay D. Evans et al.
JOURNAL OF HEREDITY (2013)
Functional and evolutionary implications of gene orthology
Toni Gabaldon et al.
NATURE REVIEWS GENETICS (2013)
The Impact of Gene Duplication, Insertion, Deletion, Lateral Gene Transfer and Sequencing Error on Orthology Inference: A Simulation Study
Daniel A. Dalquen et al.
PLOS ONE (2013)
HaMStR: Profile hidden markov model based search for orthologs in ESTs
Ingo Ebersberger et al.
BMC EVOLUTIONARY BIOLOGY (2009)
The amphioxus genome and the evolution of the chordate karyotype
Nicholas H. Putnam et al.
NATURE (2008)
Turning a hobby into a job: How duplicated genes find new functions
Gavin C. Conant et al.
NATURE REVIEWS GENETICS (2008)
Differential loss of embryonic globin genes during the radiation of placental mammals
Juan C. Opazo et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Massive horizontal gene transfer in bdelloid rotifers
Eugene A. Gladyshev et al.
SCIENCE (2008)
Consequences of genome duplication
Marie Semon et al.
CURRENT OPINION IN GENETICS & DEVELOPMENT (2007)
MEGAN analysis of metagenomic data
Daniel H. Huson et al.
GENOME RESEARCH (2007)
Local homology recognition and distance measures in linear time using compressed amino acid alphabets
RC Edgar
NUCLEIC ACIDS RESEARCH (2004)
OrthoMCL: Identification of ortholog groups for eukaryotic genomes
L Li et al.
GENOME RESEARCH (2003)
The closest BLAST hit is often not the nearest neighbor
LB Koski et al.
JOURNAL OF MOLECULAR EVOLUTION (2001)