PhylomeDB
Names
More detailed information about this field from each metasource.
PhylomeDB
metasource: Fairsharing.org
version: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:45.038954
phylomedb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:45.038954
Names
More detailed information about this field from each metasource.
PhylomeDB
metasource: Fairsharing.orgversion: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:45.038954
phylomedb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:23:45.038954
Names
More detailed information about this field from each metasource.
PhylomeDB
metasource: Fairsharing.orgversion: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:45.038954
phylomedb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:23:45.038954
PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). Researchers are able to use this resource to visualise the history of genes with the available phylogentic trees and multiple sequence alignments.
Description
More detailed information about this field from each metasource.
PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). Researchers are able to use this resource to visualise the history of genes with the available phylogentic trees and multiple sequence alignments.
metasource: Fairsharing.orgversion: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
Phylomes are complete collections of phylogenetic trees for each gene encoded in a given genome. The advent of the sequencing era has resulted in an exponential increase in the number of fully sequenced genomes. This, coupled with the improvements in tree reconstruction algorithms, have made phylome construction a tool used more and more often for the analysis of genomes. Reconstructing a phylome implies the generation of large amounts of data in the form of multiple sequence alignments and phylogenetic trees. PhylomeDB was first created to serve as storage to all this data, where users could not only download whole phylomes, but also browse through trees and alignments of their choice that had been reconstructed in the phylomes. It currently contains more than 120 public phylomes spread through the three domains of life. The amount of trees and alignments found in the database has already exceeded 1.5 million. In recent years phylomeDB has also become a referent for orthology and paralogy predictions inferred from the phylogenetic trees it stores. For each tree found in the database, phylomeDB maps speciation and duplication events to the tree from which orthology and paralogy relationships between sequences can be inferred. This is complemented by a direct link to metaPhOrs (1), which creates consensus lists of orthologs and paralogs obtained from some of the major tree databases. Also, lists of complete predictions can be downloaded for a complete phylome. One of the main features in phylomeDB is the enriched visualization of stored trees. Interactive images, created using ETE (2), allow the user to visualize additional information about the sequences being displayed and to perform several modifications such as changing the root of the tree or the order of the leaves. It also contains links that can provide the user with more information about the sequences used to reconstruct the phylome and also links to other major protein databases.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
PhylomeDB is a public database for complete catalogs of gene phylogenie. It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees. The automated pipeline used to reconstruct trees aims at providing a high-quality phylogenetic analysis of different genomes, including Maximum Likelihood tree inference, alignment trimming and evolutionary model testing.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:23:45.038954
Webpage:
http://phylomedb.orgWebpage
More detailed information about this field from each metasource.
http://phylomedb.org
metasource: Fairsharing.orgversion: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://www.phylomedb.org
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://phylomeDB.org
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:23:45.038954
Licence:
Name: OtherLicence name
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Publications:
Publications
More detailed information about this field from each metasource.
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome
PMID: 24275491
metasource: Fairsharing.org
version: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:45.038954
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
PMID: 21075798
metasource: Fairsharing.org
version: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:45.038954
PhylomeDB: a database for genome-wide collections of gene phylogenies
PMID: 17962297
metasource: Fairsharing.org
version: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:45.038954
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies
PMID: 34718760
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:45.038954
http://dx.doi.org/10.1093/nar/gkt1177
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome
PMID: 24275491
metasource: Fairsharing.org
version: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:45.038954
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
PMID: 21075798
metasource: Fairsharing.org
version: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:45.038954
PhylomeDB: a database for genome-wide collections of gene phylogenies
PMID: 17962297
metasource: Fairsharing.org
version: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:45.038954
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies
PMID: 34718760
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:45.038954
http://dx.doi.org/10.1093/nar/gkt1177
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome
PubMed citations: 131.
131 articles citing: PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome
Trypsin is a coordinate regulator of N and P nutrients in marine phytoplankton. PMID:35821503
Genome editing in the unicellular holozoan Capsaspora owczarzaki suggests a premetazoan role for the Hippo pathway in multicellular morphogenesis. PMID:35659869
Using all Gene Families Vastly Expands Data Available for Phylogenomic Inference. PMID:35642314
Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms. PMID:35451481
Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources. PMID:35255079
Candidalysins Are a New Family of Cytolytic Fungal Peptide Toxins. PMID:35073742
SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss. PMID:35021210
The transposable element-rich genome of the cereal pest Sitophilus oryzae. PMID:34749730
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. PMID:34718760
FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow. PMID:34681040
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. PMID:34537014
Orthology Clusters from Gene Trees with Possvm. PMID:34352080
Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba. PMID:34344949
Comparative Genomics Used to Predict Virulence Factors and Metabolic Genes among Monilinia Species. PMID:34201288
Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations. PMID:34129020
PAP90, a novel rice protein plays a critical role in regulation of D1 protein stability of PSII. PMID:34026296
Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase. PMID:33974913
Updates to HCOP: the HGNC comparison of orthology predictions tool. PMID:33959747
Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants? PMID:33868595
A Workflow for Selection of Single Nucleotide Polymorphic Markers for Studying of Genetics of Ischemic Stroke Outcomes. PMID:33668793
Evolution of Protein-Mediated Biomineralization in Scleractinian Corals. PMID:33633782
OrthoDB in 2020: evolutionary and functional annotations of orthologs. PMID:33196836
A new species concept for the clinically relevant Mucor circinelloides complex. PMID:33116336
Systematic analysis of bypass suppression of essential genes. PMID:32939983
In Kluyveromyces lactis a Pair of Paralogous Isozymes Catalyze the First Committed Step of Leucine Biosynthesis in Either the Mitochondria or the Cytosol. PMID:32849440
The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest. PMID:32698880
The recurrent SETBP1 c.2608G > A, p.(Gly870Ser) variant in a patient with Schinzel-Giedion syndrome: an illustrative case of the utility of whole exome sequencing in a critically ill neonate. PMID:32460883
Phylogenetic tree building in the genomic age. PMID:32424311
Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum. PMID:32359152
Perturbing proteomes at single residue resolution using base editing. PMID:32313011
The Unfolded Protein Response Modulates a Phosphoinositide-Binding Protein through the IRE1-bZIP60 Pathway. PMID:32205450
Cell cycle transcriptomics of Capsaspora provides insights into the evolution of cyclin-CDK machinery. PMID:32176685
Gene gain and loss across the metazoan tree of life. PMID:31988444
Parental origin of the allotetraploid tobacco Nicotiana benthamiana. PMID:31833111
A Novel cis Element Achieves the Same Solution as an Ancestral cis Element During Thiamine Starvation in Candida glabrata. PMID:31732505
OrthoFinder: phylogenetic orthology inference for comparative genomics. PMID:31727128
Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha. PMID:31702774
Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes. PMID:31604798
Genome Assemblies of Two Rare Opportunistic Yeast Pathogens: Diutina rugosa (syn. Candida rugosa) and Trichomonascus ciferrii (syn. Candida ciferrii). PMID:31575637
Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. PMID:31529539
Simulation data for the estimation of numerical constants for approximating pairwise evolutionary distances between amino acid sequences. PMID:31440543
OMA standalone: orthology inference among public and custom genomes and transcriptomes. PMID:31235654
Structural Characterization of Arabidopsis thaliana NAP1-Related Protein 2 (AtNRP2) and Comparison with its Homolog AtNRP1. PMID:31213016
Whole-Genome Sequencing of the Opportunistic Yeast Pathogen Candida inconspicua Uncovers Its Hybrid Origin. PMID:31105748
Candida parapsilosis: from Genes to the Bedside. PMID:30814115
Utilization of selenocysteine in early-branching fungal phyla. PMID:30742068
Matching tRNA modifications in humans to their known and predicted enzymes. PMID:30698754
Evolution of the Drosophila melanogaster Chromatin Landscape and Its Associated Proteins. PMID:30689829
Origin and diversification of the plasminogen activation system among chordates. PMID:30654737
ORTHOSCOPE: An Automatic Web Tool for Phylogenetically Inferring Bilaterian Orthogroups with User-Selected Taxa. PMID:30517749
iHam and pyHam: visualizing and processing hierarchical orthologous groups. PMID:30508066
Comparative Transcriptomics Highlights New Features of the Iron Starvation Response in the Human Pathogen Candida glabrata. PMID:30505294
CAARS: comparative assembly and annotation of RNA-Seq data. PMID:30452539
Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum. PMID:30415838
OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. PMID:30395283
Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life. PMID:30371900
Efficient inference of homologs in large eukaryotic pan-proteomes. PMID:30257640
DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference. PMID:30217139
Systematic Analysis of Mouse Genome Reveals Distinct Evolutionary and Functional Properties Among Circadian and Ultradian Genes. PMID:30190679
FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. PMID:30152809
mTOR Complex 1 Implicated in Aphid/Buchnera Host/Symbiont Integration. PMID:30049746
The Evolutionary Consequences of Transposon-Related Pericentromer Expansion in Melon. PMID:29901717
Saccharomyces cerevisiae Differential Functionalization of Presumed ScALT1 and ScALT2 Alanine Transaminases Has Been Driven by Diversification of Pyridoxal Phosphate Interactions. PMID:29867852
Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events. PMID:29370802
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. PMID:29106550
Microbial genome analysis: the COG approach. PMID:28968633
Regulatory Mechanisms of a Highly Pectinolytic Mutant of Penicillium occitanis and Functional Analysis of a Candidate Gene in the Plant Pathogen Fusarium oxysporum. PMID:28951729
Tremblaya phenacola PPER: an evolutionary beta-gammaproteobacterium collage. PMID:28914880
KinFin: Software for Taxon-Aware Analysis of Clustered Protein Sequences. PMID:28866640
Eukaryotic transporters for hydroxyderivatives of benzoic acid. PMID:28827635
Fungal Genomes and Insights into the Evolution of the Kingdom. PMID:28820125
Genome-wide signatures of complex introgression and adaptive evolution in the big cats. PMID:28776029
Predicting Amino Acid Substitution Probabilities Using Single Nucleotide Polymorphisms. PMID:28754661
Evolutionary Diversification of Alanine Transaminases in Yeast: Catabolic Specialization and Biosynthetic Redundancy. PMID:28694796
Hybridization and emergence of virulence in opportunistic human yeast pathogens. PMID:28681409
OrthoReD: a rapid and accurate orthology prediction tool with low computational requirement. PMID:28633662
Transcription Factors in Fungi: TFome Dynamics, Three Major Families, and Dual-Specificity TFs. PMID:28523015
Transcriptologs: A Transcriptome-Based Approach to Predict Orthology Relationships. PMID:28469416
Three, two, one yeast fatty acid desaturases: regulation and function. PMID:28390014
HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency. PMID:28358052
Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. PMID:28190401
Variability among Cucurbitaceae species (melon, cucumber and watermelon) in a genomic region containing a cluster of NBS-LRR genes. PMID:28178932
Protein Bioinformatics Databases and Resources. PMID:28150231
Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone. PMID:27965389
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. PMID:27964752
Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol. PMID:27897972
HieranoiDB: a database of orthologs inferred by Hieranoid. PMID:27742821
Mitochondrial Carriers Link the Catabolism of Hydroxyaromatic Compounds to the Central Metabolism in Candida parapsilosis. PMID:27707801
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. PMID:27664130
Evolutionary genomics of yeast pathogens in the Saccharomycotina. PMID:27493146
Computational assessment of feature combinations for pathogenic variant prediction. PMID:27468419
ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods. PMID:27242037
Holding it together: rapid evolution and positive selection in the synaptonemal complex of Drosophila. PMID:27150275
Phylogenetic Profiling for Probing the Modular Architecture of the Human Genome. PMID:27135799
Standardized benchmarking in the quest for orthologs. PMID:27043882
Partial Decay of Thiamine Signal Transduction Pathway Alters Growth Properties of Candida glabrata. PMID:27015653
PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins. PMID:26980520
PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya. PMID:26980519
ncRNA orthologies in the vertebrate lineage. PMID:26980512
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. PMID:26921390
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. PMID:26911872
Hypothesis: Paralog Formation from Progenitor Proteins and Paralog Mutagenesis Spur the Rapid Evolution of Telomere Binding Proteins. PMID:26904098
Ensembl comparative genomics resources. PMID:26896847
Homodimeric PHD Domain-containing Rco1 Subunit Constitutes a Critical Interaction Hub within the Rpd3S Histone Deacetylase Complex. PMID:26747610
Genome sequencing and secondary metabolism of the postharvest pathogen Penicillium griseofulvum. PMID:26729047
Structural Motifs Critical for In Vivo Function and Stability of the RecQ-Mediated Genome Instability Protein Rmi1. PMID:26717309
Horizontal acquisition of toxic alkaloid synthesis in a clade of plant associated fungi. PMID:26688468
The birth of a deadly yeast: tracing the evolutionary emergence of virulence traits in Candida glabrata. PMID:26684722
Target selection by natural and redesigned PUF proteins. PMID:26668354
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. PMID:26582926
The Leishmania metaphylome: a comprehensive survey of Leishmania protein phylogenetic relationships. PMID:26518129
The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis. PMID:26517373
SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. PMID:26516187
Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage. PMID:26252497
Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream. PMID:26133389
PlantOrDB: a genome-wide ortholog database for land plants and green algae. PMID:26112452
Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. PMID:26108467
Domain similarity based orthology detection. PMID:25968113
OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. PMID:25964301
Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants. PMID:25887590
The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives. PMID:25873387
Origin and evolution of metabolic sub-cellular compartmentalization in eukaryotes. PMID:25869000
STBase: one million species trees for comparative biology. PMID:25679219
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. PMID:25504731
Whole-genome analyses resolve early branches in the tree of life of modern birds. PMID:25504713
Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi. PMID:25480150
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. PMID:25399418
Genenames.org: the HGNC resources in 2015. PMID:25361968
Computational biophysical, biochemical, and evolutionary signature of human R-spondin family proteins, the member of canonical Wnt/β-catenin signaling pathway. PMID:25276837
Genome-wide annotation and functional identification of aphid GLUT-like sugar transporters. PMID:25091229
Big data and other challenges in the quest for orthologs. PMID:25064571 -
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
PubMed citations: 95.
95 articles citing: PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants. PMID:34253868
Comparative Genomics Used to Predict Virulence Factors and Metabolic Genes among Monilinia Species. PMID:34201288
An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice. PMID:32899740
Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum. PMID:32359152
MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life. PMID:32343307
Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of Burkholderia cenocepacia J2315 and Other Members of the B. cepacia Complex. PMID:32098200
Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha. PMID:31702774
Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes. PMID:31604798
Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. PMID:31529539
Evolutionary and functional patterns of shared gene neighbourhood in fungi. PMID:31527797
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. PMID:30418610
Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication. PMID:29746697
Practical considerations for plant phylogenomics. PMID:29732268
Genome Sequence of the Brown Rot Fungal Pathogen Monilinia laxa. PMID:29700136
Probing the Phylogenomics and Putative Pathogenicity Genes of Pythium insidiosum by Oomycete Genome Analyses. PMID:29515152
Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events. PMID:29370802
Regulatory Mechanisms of a Highly Pectinolytic Mutant of Penicillium occitanis and Functional Analysis of a Candidate Gene in the Plant Pathogen Fusarium oxysporum. PMID:28951729
Three, two, one yeast fatty acid desaturases: regulation and function. PMID:28390014
Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes. PMID:28066338
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. PMID:27964752
SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees. PMID:27635331
Efficient Gene Tree Correction Guided by Genome Evolution. PMID:27513924
Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems. PMID:27413050
Computational Identification of the Paralogs and Orthologs of Human Cytochrome P450 Superfamily and the Implication in Drug Discovery. PMID:27367670
Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences. PMID:27289096
The link between orthology relations and gene trees: a correction perspective. PMID:27087831
Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life. PMID:26951068
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. PMID:26911872
Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry. PMID:26840490
Genome sequencing and secondary metabolism of the postharvest pathogen Penicillium griseofulvum. PMID:26729047
Horizontal acquisition of toxic alkaloid synthesis in a clade of plant associated fungi. PMID:26688468
Contrasting Genomic Diversity in Two Closely Related Postharvest Pathogens: Penicillium digitatum and Penicillium expansum. PMID:26672008
Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection. PMID:26627243
An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species. PMID:26605337
The Leishmania metaphylome: a comprehensive survey of Leishmania protein phylogenetic relationships. PMID:26518129
The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis. PMID:26517373
Reconstructing a SuperGeneTree minimizing reconciliation. PMID:26451911
Role of Cln1 during melanization of Cryptococcus neoformans. PMID:26322026
C5orf30 is a negative regulator of tissue damage in rheumatoid arthritis. PMID:26316022
Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage. PMID:26252497
Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization. PMID:26194102
Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. PMID:26108467
Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus. PMID:26076695
Evolution of the SH3 Domain Specificity Landscape in Yeasts. PMID:26068101
A meta-approach for improving the prediction and the functional annotation of ortholog groups. PMID:25573073
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. PMID:25504731
The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima. PMID:25423365
Mutational bias is the driving force for shaping the synonymous codon usage pattern of alternatively spliced genes in rice (Oryza sativa L.). PMID:25407289
A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PMID:25369365
Genome-wide identification and evolutionary analysis of positively selected miRNA genes in domesticated rice. PMID:25362560
Computational biophysical, biochemical, and evolutionary signature of human R-spondin family proteins, the member of canonical Wnt/β-catenin signaling pathway. PMID:25276837
Polytomy refinement for the correction of dubious duplications in gene trees. PMID:25161242
Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina). PMID:25121733
Phylogenetic analysis and evolutionary origins of DNA polymerase X-family members. PMID:25112931
morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring. PMID:25096057
Systematic phenotyping of a large-scale Candida glabrata deletion collection reveals novel antifungal tolerance genes. PMID:24945925
The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest. PMID:24834124
QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors. PMID:24586435
Extreme population differences in the human zinc transporter ZIP4 (SLC39A4) are explained by positive selection in Sub-Saharan Africa. PMID:24586184
A phylogenomics approach for selecting robust sets of phylogenetic markers. PMID:24476915
Complete DNA sequence of Kuraishia capsulata illustrates novel genomic features among budding yeasts (Saccharomycotina). PMID:24317973
eggNOG v4.0: nested orthology inference across 3686 organisms. PMID:24297252
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. PMID:24275491
Unexpected genomic variability in clinical and environmental strains of the pathogenic yeast Candida parapsilosis. PMID:24259314
TreeFam v9: a new website, more species and orthology-on-the-fly. PMID:24194607
SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans. PMID:24194593
The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution. PMID:24068976
Comparative genomics of emerging pathogens in the Candida glabrata clade. PMID:24034898
The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification. PMID:23685612
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity. PMID:23677614
Tyrosine pathway regulation is host-mediated in the pea aphid symbiosis during late embryonic and early larval development. PMID:23575215
Functional and evolutionary implications of gene orthology. PMID:23552219
Measuring guide-tree dependency of inferred gaps in progressive aligners. PMID:23435067
Comparative transcriptomics of early dipteran development. PMID:23432914
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. PMID:23180791
Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus. PMID:23171342
The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite's biology. PMID:23148687
Mutational bias and translational selection shaping the codon usage pattern of tissue-specific genes in rice. PMID:23144748
Genome-scale coestimation of species and gene trees. PMID:23132911
R4 regulators of G protein signaling (RGS) identify an ancient MHC-linked synteny group. PMID:23129146
CysQ of Cryptosporidium parvum, a Protozoa, May Have Been Acquired from Bacteria by Horizontal Gene Transfer. PMID:23105923
Proteomic characterization of phagosomal membrane microdomains during phagolysosome biogenesis and evolution. PMID:22915823
The chordate proteome history database. PMID:22904610
The genome of melon (Cucumis melo L.). PMID:22753475
QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence. PMID:22726705
Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi. PMID:22651672
Composition and evolution of the vertebrate and mammalian selenoproteomes. PMID:22479358
EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data. PMID:22267905
Roundup 2.0: enabling comparative genomics for over 1800 genomes. PMID:22247275
Global analysis of serine-threonine protein kinase genes in Neurospora crassa. PMID:21965514
Orthology prediction methods: a quality assessment using curated protein families. PMID:21853451
MultiMSOAR 2.0: an accurate tool to identify ortholog groups among multiple genomes. PMID:21712981
Computational methods for Gene Orthology inference. PMID:21690100
PhyleasProg: a user-oriented web server for wide evolutionary analyses. PMID:21531699
TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees. PMID:21335609 -
PhylomeDB: a database for genome-wide collections of gene phylogenies
PubMed citations: 55.
55 articles citing: PhylomeDB: a database for genome-wide collections of gene phylogenies
OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins. PMID:35610035
SHOOT: phylogenetic gene search and ortholog inference. PMID:35346327
New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. PMID:34897464
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. PMID:34718760
Integration of 1:1 orthology maps and updated datasets into Echinobase. PMID:34010390
MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life. PMID:32343307
The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs. PMID:31454312
Orthonome - a new pipeline for predicting high quality orthologue gene sets applicable to complete and draft genomes. PMID:28859620
Towards Consensus Gene Ages. PMID:27259914
Hypothesis: Paralog Formation from Progenitor Proteins and Paralog Mutagenesis Spur the Rapid Evolution of Telomere Binding Proteins. PMID:26904098
Ortholog-Finder: A Tool for Constructing an Ortholog Data Set. PMID:26782935
Role of Cln1 during melanization of Cryptococcus neoformans. PMID:26322026
Genome-Wide Collation of the Plasmodium falciparum WDR Protein Superfamily Reveals Malarial Parasite-Specific Features. PMID:26043001
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. PMID:25504731
Computational biophysical, biochemical, and evolutionary signature of human R-spondin family proteins, the member of canonical Wnt/β-catenin signaling pathway. PMID:25276837
Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score. PMID:24885064
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. PMID:24275491
The family structure of the Mucorales: a synoptic revision based on comprehensive multigene-genealogies. PMID:24027347
Computational discovery of transcriptional regulatory modules in fungal ribosome biogenesis genes reveals novel sequence and function patterns. PMID:23555806
Inferring hierarchical orthologous groups from orthologous gene pairs. PMID:23342000
QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence. PMID:22726705
The use of evolutionary patterns in protein annotation. PMID:22633559
Revealing mammalian evolutionary relationships by comparative analysis of gene clusters. PMID:22454131
Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life. PMID:22399455
Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase. PMID:22356826
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. PMID:22096231
Global analysis of serine-threonine protein kinase genes in Neurospora crassa. PMID:21965514
Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles. PMID:21943375
An integrative approach to ortholog prediction for disease-focused and other functional studies. PMID:21880147
Ortholog identification in the presence of domain architecture rearrangement. PMID:21712343
CycADS: an annotation database system to ease the development and update of BioCyc databases. PMID:21474551
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. PMID:21149260
OMA 2011: orthology inference among 1000 complete genomes. PMID:21113020
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. PMID:21075798
Genome-wide comparative gene family classification. PMID:20976221
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. PMID:20972218
Molecular characterization of the evolution of phagosomes. PMID:20959821
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. PMID:20626897
Bioinformatic Identification of Novel Methyltransferases. PMID:20582239
GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. PMID:20534164
AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome. PMID:20482635
Getting started in gene orthology and functional analysis. PMID:20361041
Historical constraints on vertebrate genome evolution. PMID:20333219
Genome sequence of the pea aphid Acyrthosiphon pisum. PMID:20186266
Immunity and other defenses in pea aphids, Acyrthosiphon pisum. PMID:20178569
2x genomes--depth does matter. PMID:20144222
ETE: a python Environment for Tree Exploration. PMID:20070885
Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence. PMID:20025735
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. PMID:19900971
PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome. PMID:19892824
Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions. PMID:19805074
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. PMID:19505945
Berkeley PHOG: PhyloFacts orthology group prediction web server. PMID:19435885
The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome. PMID:19190756
Large-scale assignment of orthology: back to phylogenetics? PMID:18983710 -
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies
PubMed citations: 4.
4 articles citing: PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies
Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad. PMID:35583263
The Quest for Orthologs orthology benchmark service in 2022. PMID:35552456
PhyloCloud: an online platform for making sense of phylogenomic data. PMID:35544233
Genome analysis of five recently described species of the CUG-Ser clade uncovers Candida theae as a new hybrid lineage with pathogenic potential in the Candida parapsilosis species complex. PMID:35438177 - http://dx.doi.org/10.1093/nar/gkt1177
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genome
metasource: Fairsharing.org
version: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
orthologous
metasource: Fairsharing.org
version: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
taxonomic classification
metasource: Fairsharing.org
version: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
general genomics databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
human and other vertebrate genomes
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
model organisms, comparative genomics
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
phylogeny
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:45.038954
pathology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:45.038954
phylogenomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:45.038954
model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:45.038954
Tags
More detailed information about this field from each metasource.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
orthologous
metasource: Fairsharing.orgversion: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
taxonomic classification
metasource: Fairsharing.orgversion: FAIRsharing.org: PhylomeDB; PhylomeDB; DOI: https://doi.org/10.25504/FAIRsharing.7hxxc4; Last edited: April 26, 2021, 9:30 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
general genomics databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
human and other vertebrate genomes
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
model organisms, comparative genomics
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
phylogeny
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:23:45.038954
pathology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:23:45.038954
phylogenomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:23:45.038954
model organisms
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:23:45.038954
genome orthology taxonomic classification genomics general genomics human and other vertebrate genomes model organisms phylogeny pathology phylogenomics model organisms
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