FastOMA is a scalable software package to infer orthology relationship.
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Sep 14, 2026 - Python
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orthology
Here are 37 public repositories matching this topic...
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
bioinformatics bioinformatics-pipeline phylogenetics orthology homology ncbi-sra gene-sequence-retrieval
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Apr 2, 2021 - Python
a broadly applicable tool for automated gene identification and retrieval
python bioinformatics genomics evolution phylogenetics orthology-inference phylogenomics evolutionary-biology orthology orthology-assignments
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Jun 16, 2026 - Python
Phyling: phylogenetic inference from annotated genomes
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Sep 7, 2026 - Python
a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
python bioinformatics genomics evolution phylogenetics orthology-inference phylogenomics evolutionary-biology orthology orthology-assignments
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Jul 13, 2026 - Python
An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵
python shell bash data-science bioinformatics genetics biology ftp sge phylogenetics blast orthologues qsub orthology-inference ncbi sequence-alignment pbs orthologs orthology biosql
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Sep 6, 2026 - Python
a python package for automated generation of phylogenetic trees from genbank files
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Apr 9, 2026 - Python
Workflow for identifying and classifying homologous gene/protein sequences
bioinformatics python3 biopython gene-families genome-annotation blast comparative-genomics molecular-evolution similarity-search protein-families orthology homology snakemake-workflow hmmer3 transcriptome-annotation coulson-plot
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Oct 6, 2025 - Python
Feature-aware Directed OrtholoG search
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Aug 26, 2026 - Python
Tree-based orthology inference with functionality for reducing contamination
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May 22, 2026 - Python
Feature-aware orthology prediction tool. Provided data package: Quest for Orthologs reference gene sets 2019.
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Oct 6, 2020 - Perl
Collection of scripts for gene age sorting and multi-omics data mining and analysis
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Sep 17, 2020 - R
Reproducible phylogenomics pipeline that builds partitioned species trees from BUSCO v5 results.
python bioinformatics genomics comparative-genomics orthology-inference phylogenomics phylogenomics-pipeline species-tree orthology completeness busco genome-assessment
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Jan 19, 2026 - Python
Research compendium for Viscardi et al, 2020.
bioinformatics r evolution network-analysis kegg igraph orthology expression-atlas research-compendium stringdb neurotransmission
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Feb 20, 2026 - TeX
Supplementary data and pipelines for analyzing genome gene content data and morphology to create various phylogenies.
bash-script proteome genomes phylogeny homology-search orthology genomes-comparison revbayes full-genome
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May 4, 2023 - R
This curation tool allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions.
paint gene annotation owl ontology phylogenetics curation annotation-tool geneontology functional-annotation orthology
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May 9, 2017 - Java
Local web platform for orthology-based proteome/proteomics comparison and Gene Ontology enrichment. Run OrthoFinder, explore orthogroups, and perform GO enrichment locally with publication-ready outputs.
bioinformatics gene-ontology orthology bioinformatics-tool proteomics-data-analysis orthogroups go-enrichment
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Sep 13, 2026 - Python
Vivarium 2.0: actively maintained comparative-genomics workflow skills for Claude Code and Codex, with event-sourced execution, crash-safe recovery, ANI/AAI, orthology, synteny, phylogeny, QC/annotation, and publication-ready figures.
bioinformatics genomics reproducible-research workflow-engine event-sourcing phylogenetics scientific-computing comparative-genomics synteny codex ani ai-agents aai orthology research-software crash-recovery agentic-workflows claude-code
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Jul 20, 2026 - Python
A stand-alone tool for evaluating simple statistics of orthologs
phylogenetics orthology-inference phylogenetic-tree orthology orthology-assignments orthology-relationships
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Sep 20, 2021 - Python
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