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OMA standalone: orthology inference among public and custom genomes and transcriptomes

https://doi.org/10.1101/397752
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/11554714_6openalex-snapshot
OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements
inferredcites →https://doi.org/10.1007/s13127-011-0044-4openalex-snapshot
Higher-level metazoan relationships: recent progress and remaining questions
inferredcites →https://doi.org/10.1016/0022-2836(81)90087-5openalex-snapshot
Identification of common molecular subsequences
inferredcites →https://doi.org/10.1016/j.cub.2015.03.034openalex-snapshot
A Transcriptomic-Phylogenomic Analysis of the Evolutionary Relationships of Flatworms
inferredcites →https://doi.org/10.1016/j.cub.2015.07.060openalex-snapshot
Phylogenomic Insights into Animal Evolution
inferredcites →https://doi.org/10.1016/j.drudis.2011.02.016openalex-snapshot
In silico repositioning of approved drugs for rare and neglected diseases
inferredcites →https://doi.org/10.1016/j.tig.2007.08.014openalex-snapshot
A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages
inferredcites →https://doi.org/10.1038/nature06614openalex-snapshot
Broad phylogenomic sampling improves resolution of the animal tree of life
inferredcites →https://doi.org/10.1038/nature09676openalex-snapshot
Acoelomorph flatworms are deuterostomes related to Xenoturbella
inferredcites →https://doi.org/10.1038/nature10382openalex-snapshot
Phylogenomics reveals deep molluscan relationships
inferredcites →https://doi.org/10.1038/nature12031openalex-snapshot
The genomes of four tapeworm species reveal adaptations to parasitism
inferredcites →https://doi.org/10.1038/nmeth.3830openalex-snapshot
Standardized benchmarking in the quest for orthologs
inferredcites →https://doi.org/10.1038/nprot.2013.084openalex-snapshot
De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
inferredcites →https://doi.org/10.1038/nrg3456openalex-snapshot
Functional and evolutionary implications of gene orthology
inferredcites →https://doi.org/10.1038/s41598-017-00132-9openalex-snapshot
Comparative genomics reveals contraction in olfactory receptor genes in bats
inferredcites →https://doi.org/10.1073/pnas.0915125107openalex-snapshot
Repositioning of an existing drug for the neglected tropical disease Onchocerciasis
inferredcites →https://doi.org/10.1073/pnas.1618463114openalex-snapshot
Integrative modeling of gene and genome evolution roots the archaeal tree of life
inferredcites →https://doi.org/10.1073/pnas.96.8.4285openalex-snapshot
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
inferredcites →https://doi.org/10.1093/bib/bbr025openalex-snapshot
Letter to the Editor: SeqXML and OrthoXML: standards for sequence and orthology information
inferredcites →https://doi.org/10.1093/bib/bbr034openalex-snapshot
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees
inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btr026openalex-snapshot
Quality control and preprocessing of metagenomic datasets
inferredcites →https://doi.org/10.1093/bioinformatics/bts050openalex-snapshot
Toward community standards in the quest for orthologs
inferredcites →https://doi.org/10.1093/bioinformatics/bts565openalex-snapshot
CD-HIT: accelerated for clustering the next-generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu492openalex-snapshot
Big data and other challenges in the quest for orthologs
inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
inferredcites →https://doi.org/10.1093/bioinformatics/btx229openalex-snapshot
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference
inferredcites →https://doi.org/10.1093/bioinformatics/btx542openalex-snapshot
Gearing up to handle the mosaic nature of life in the quest for orthologs
inferredcites →https://doi.org/10.1093/gbe/evt132openalex-snapshot
Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals
inferredcites →https://doi.org/10.1093/icb/icx072openalex-snapshot
Current Understanding of Ecdysozoa and its Internal Phylogenetic Relationships
inferredcites →https://doi.org/10.1093/molbev/msn019openalex-snapshot
Phylogenetic Position of Nemertea Derived from Phylogenomic Data
inferredcites →https://doi.org/10.1093/molbev/msu108openalex-snapshot
Evaluating Topological Conflict in Centipede Phylogeny Using Transcriptomic Data Sets
inferredcites →https://doi.org/10.1093/molbev/msu143openalex-snapshot
Platyzoan Paraphyly Based on Phylogenomic Data Supports a Noncoelomate Ancestry of Spiralia
inferredcites →https://doi.org/10.1093/molbev/msu235openalex-snapshot
Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkj123openalex-snapshot
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
inferredcites →https://doi.org/10.1093/nar/gkl433openalex-snapshot
Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits
inferredcites →https://doi.org/10.1093/nar/gkr1100openalex-snapshot
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
inferredcites →https://doi.org/10.1093/nar/gks1006openalex-snapshot
MBGD update 2013: the microbial genome database for exploring the diversity of microbial world
inferredcites →https://doi.org/10.1093/nar/gkt1177openalex-snapshot
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome
inferredcites →https://doi.org/10.1093/nar/gkt399openalex-snapshot
The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification
inferredcites →https://doi.org/10.1093/nar/gku1158openalex-snapshot
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements
inferredcites →https://doi.org/10.1093/nar/gku1203openalex-snapshot
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
inferredcites →https://doi.org/10.1093/nar/gkv1248openalex-snapshot
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
inferredcites →https://doi.org/10.1093/nar/gkw1119openalex-snapshot
OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs
inferredcites →https://doi.org/10.1093/nar/gkw1138openalex-snapshot
PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements
inferredcites →https://doi.org/10.1093/nar/gkx1019openalex-snapshot
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces
inferredcites →https://doi.org/10.1093/nar/gkx1098openalex-snapshot
Ensembl 2018
inferredcites →https://doi.org/10.1093/sysbio/syt022openalex-snapshot
PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment
inferredcites →https://doi.org/10.1093/sysbio/syw079openalex-snapshot
Phylogenomics of Lophotrochozoa with Consideration of Systematic Error
inferredcites →https://doi.org/10.1098/rsos.150065openalex-snapshot
Unnoticed in the tropics: phylogenomic resolution of the poorly known arachnid order Ricinulei (Arachnida)
inferredcites →https://doi.org/10.1098/rspb.2009.0896openalex-snapshot
Assessing the root of bilaterian animals with scalable phylogenomic methods
inferredcites →https://doi.org/10.1101/gr.073585.107openalex-snapshot
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
inferredcites →https://doi.org/10.1101/gr.1224503openalex-snapshot
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
inferredcites →https://doi.org/10.1139/z03-214openalex-snapshot
Molecular phylogeny of the Platyhelminthes
inferredcites →https://doi.org/10.1146/annurev-ecolsys-120213-091627openalex-snapshot
Animal Phylogeny and Its Evolutionary Implications
inferredcites →https://doi.org/10.1186/1471-2105-12-11openalex-snapshot
OrthoInspector: comprehensive orthology analysis and visual exploration
inferredcites →https://doi.org/10.1186/1471-2105-9-518openalex-snapshot
Algorithm of OMA for large-scale orthology inference
inferredcites →https://doi.org/10.1186/1471-2148-9-157openalex-snapshot
HaMStR: Profile hidden markov model based search for orthologs in ESTs
inferredcites →https://doi.org/10.1186/1756-0500-1-107openalex-snapshot
SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ×86/SSE2
inferredcites →https://doi.org/10.1186/s12915-018-0486-7openalex-snapshot
A software tool ‘CroCo’ detects pervasive cross-species contamination in next generation sequencing data
inferredcites →https://doi.org/10.1371/journal.pbio.1000602openalex-snapshot
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
inferredcites →https://doi.org/10.1371/journal.pcbi.1000262openalex-snapshot
Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods
inferredcites →https://doi.org/10.1371/journal.pcbi.1002514openalex-snapshot
Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs
inferredcites →https://doi.org/10.1371/journal.pntd.0000464openalex-snapshot
A Novel Biological Activity of Praziquantel Requiring Voltage-Operated Ca2+ Channel β Subunits: Subversion of Flatworm Regenerative Polarity
inferredcites →https://doi.org/10.1371/journal.pone.0041175openalex-snapshot
The Natural History of Class I Primate Alcohol Dehydrogenases Includes Gene Duplication, Gene Loss, and Gene Conversion
inferredcites →https://doi.org/10.1371/journal.pone.0053786openalex-snapshot
Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs
inferredcites →https://doi.org/10.7554/elife.05503openalex-snapshot
Nuclear genomic signals of the ‘microturbellarian’ roots of platyhelminth evolutionary innovation
inferredcites →https://doi.org/10.7717/peerj.1719openalex-snapshot
Spider phylogenomics: untangling the Spider Tree of Life
inferredcites →https://doi.org/10.7717/peerj.2951openalex-snapshot
Genomic and transcriptomic resources for assassin flies including the complete genome sequence ofProctacanthus coquilletti(Insecta: Diptera: Asilidae) and 16 representative transcriptomes

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Phylogenomic interrogation resolves the backbone of the Pseudoscorpiones tree of life
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An episodic burst of massive genomic rearrangements and the origin of non-marine annelids
inferred← citeshttps://doi.org/10.1038/s41576-020-0233-0openalex-snapshot
Phylogenetic tree building in the genomic age
inferred← citeshttps://doi.org/10.1038/s41586-024-07070-3openalex-snapshot
The hagfish genome and the evolution of vertebrates
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Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree
inferred← citeshttps://doi.org/10.1038/s41588-024-01781-zopenalex-snapshot
Complexin-1 enhances ultrasound neurotransmission in the mammalian auditory pathway
inferred← citeshttps://doi.org/10.1038/s41594-025-01649-8openalex-snapshot
Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses
inferred← citeshttps://doi.org/10.1186/s12864-020-6764-0openalex-snapshot
Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum
inferred← citeshttps://doi.org/10.1186/s13015-023-00238-yopenalex-snapshot
Efficient gene orthology inference via large-scale rearrangements
inferred← citeshttps://doi.org/10.21203/rs.3.rs-1254205/v1openalex-snapshot
From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala)
inferred← citeshttps://doi.org/10.21203/rs.3.rs-4346819/v1openalex-snapshot
A punctuated burst of massive genomic rearrangements by chromosome shattering and the origin of non-marine annelids
inferred← citeshttps://doi.org/10.7554/elife.88229.1.sa0openalex-snapshot
Reviewer #3 (Public Review): Broad functional profiling of fission yeast proteins using phenomics and machine learning
inferred← citeshttps://doi.org/10.7554/elife.88229.1.sa3openalex-snapshot
eLife Assessment: Broad functional profiling of fission yeast proteins using phenomics and machine learning
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