MetaPhors
MetaPhOrs is a public repository of phylogeny-based orthologs and paralogs that were computed using phylogenetic trees available in twelve public repositories. Currently, over 117,131,162 of unique homologs are deposited in MetaPhOrs database. These predictions were retrieved from 8,246,911 Maximum Likelihood trees for 4,094 species. For each prediction, MetaPhOrs provides a Consistency Score and Evidence Level describing its goodness, together with number of trees and links to their source databases.
Description
More detailed information about this field from each metasource.
MetaPhOrs is a public repository of phylogeny-based orthologs and paralogs that were computed using phylogenetic trees available in twelve public repositories. Currently, over 117,131,162 of unique homologs are deposited in MetaPhOrs database. These predictions were retrieved from 8,246,911 Maximum Likelihood trees for 4,094 species. For each prediction, MetaPhOrs provides a Consistency Score and Evidence Level describing its goodness, together with number of trees and links to their source databases.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:23.360357
Webpage:
http://orthology.phylomedb.org/Webpage
More detailed information about this field from each metasource.
http://orthology.phylomedb.org/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:23.360357
Licence:
Name: OtherLicence name
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Publications:
Publications
More detailed information about this field from each metasource.
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score
PMID: 21149260
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:23.360357
MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life
PMID: 32343307
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:23.360357
Publications
More detailed information about this field from each metasource.
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score
PMID: 21149260
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:23.360357
MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life
PMID: 32343307
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:23.360357
-
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score
PubMed citations: 65.
65 articles citing: MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score
A Prioritized and Validated Resource of Mitochondrial Proteins in Plasmodium Identifies Unique Biology. PMID:34494883
Role of epigenetics in unicellular to multicellular transition in Dictyostelium. PMID:33947439
A Workflow for Selection of Single Nucleotide Polymorphic Markers for Studying of Genetics of Ischemic Stroke Outcomes. PMID:33668793
Structure and function of the vacuolar Ccc1/VIT1 family of iron transporters and its regulation in fungi. PMID:33304466
Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes. PMID:32935832
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
Draft genome of the European medicinal leech Hirudo medicinalis (Annelida, Clitellata, Hirudiniformes) with emphasis on anticoagulants. PMID:32555498
Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker. PMID:32440005
MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life. PMID:32343307
The in vivo ISGylome links ISG15 to metabolic pathways and autophagy upon Listeria monocytogenes infection. PMID:31772204
Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. PMID:31599721
Advances and Applications in the Quest for Orthologs. PMID:31241141
Candida parapsilosis: from Genes to the Bedside. PMID:30814115
Evolution of the Drosophila melanogaster Chromatin Landscape and Its Associated Proteins. PMID:30689829
Assigning confidence scores to homoeologs using fuzzy logic. PMID:30648004
Automated selection of homologs to track the evolutionary history of proteins. PMID:30453878
Nonsense-mediated mRNA decay involves two distinct Upf1-bound complexes. PMID:30275269
OrthoList 2: A New Comparative Genomic Analysis of Human and Caenorhabditis elegans Genes. PMID:30120140
AOP-DB: A database resource for the exploration of Adverse Outcome Pathways through integrated association networks. PMID:29454060
ECOdrug: a database connecting drugs and conservation of their targets across species. PMID:29140522
Global Analysis of Membrane-associated Protein Oligomerization Using Protein Correlation Profiling. PMID:28887381
Orthonome - a new pipeline for predicting high quality orthologue gene sets applicable to complete and draft genomes. PMID:28859620
Transcription Factors in Fungi: TFome Dynamics, Three Major Families, and Dual-Specificity TFs. PMID:28523015
WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning. PMID:27812085
Secondary metabolite gene clusters in the entomopathogen fungus Metarhizium anisopliae: genome identification and patterns of expression in a cuticle infection model. PMID:27801295
Mitochondrial Carriers Link the Catabolism of Hydroxyaromatic Compounds to the Central Metabolism in Candida parapsilosis. PMID:27707801
Efficient Gene Tree Correction Guided by Genome Evolution. PMID:27513924
Towards Consensus Gene Ages. PMID:27259914
ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods. PMID:27242037
The link between orthology relations and gene trees: a correction perspective. PMID:27087831
Standardized benchmarking in the quest for orthologs. PMID:27043882
Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications. PMID:27028541
PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya. PMID:26980519
The birth of a deadly yeast: tracing the evolutionary emergence of virulence traits in Candida glabrata. PMID:26684722
An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species. PMID:26605337
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
Reconstructing a SuperGeneTree minimizing reconciliation. PMID:26451911
Applications of comparative evolution to human disease genetics. PMID:26338499
Evolution of the SH3 Domain Specificity Landscape in Yeasts. PMID:26068101
OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. PMID:25964301
Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference. PMID:25711833
A meta-approach for improving the prediction and the functional annotation of ortholog groups. PMID:25573073
Orthology and paralogy constraints: satisfiability and consistency. PMID:25572629
Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer. PMID:25487147
FLAGS, frequently mutated genes in public exomes. PMID:25466818
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
The TRiC/CCT chaperone is implicated in Alzheimer's disease based on patient GWAS and an RNAi screen in Aβ-expressing Caenorhabditis elegans. PMID:25080104
Big data and other challenges in the quest for orthologs. PMID:25064571
Genome comparison of Candida orthopsilosis clinical strains reveals the existence of hybrids between two distinct subspecies. PMID:24747362
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
TPMS: a set of utilities for querying collections of gene trees. PMID:23530580
Mutational bias and translational selection shaping the codon usage pattern of tissue-specific genes in rice. PMID:23144748
Orthology relations, symbolic ultrametrics, and cographs. PMID:22456957
Toward community standards in the quest for orthologs. PMID:22332236
Dissecting plant genomes with the PLAZA comparative genomics platform. PMID:22198273
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. PMID:22096231
Orthology prediction methods: a quality assessment using curated protein families. PMID:21853451
Computational methods for Gene Orthology inference. PMID:21690100
QuartetS: a fast and accurate algorithm for large-scale orthology detection. PMID:21572104
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. PMID:21075798 -
MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life
PubMed citations: 8.
8 articles citing: MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life
Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources. PMID:35255079
Leveraging machine learning essentiality predictions and chemogenomic interactions to identify antifungal targets. PMID:34764269
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. PMID:34718760
Essential shared and species-specific features of mammalian oocyte maturation-associated transcriptome changes impacting oocyte physiology. PMID:33881934
Nuclear RNA purification by flow cytometry to study nuclear processes in plants. PMID:33659901
Structure and function of the vacuolar Ccc1/VIT1 family of iron transporters and its regulation in fungi. PMID:33304466
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
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More detailed information about this field from each metasource.
phylogenomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:23.360357
phylogenetics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:23.360357
evolutionary biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:23.360357
phylogeny
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:23.360357
Tags
More detailed information about this field from each metasource.
phylogenomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:23.360357
phylogenetics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:23.360357
evolutionary biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:23.360357
phylogeny
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:23.360357
phylogenomics phylogenetics evolutionary biology phylogeny
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