orthology

FastOMA is a scalable software package to infer orthology relationship.

A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly

a broadly applicable tool for automated gene identification and retrieval

Phyling: phylogenetic inference from annotated genomes

a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

a python package for automated generation of phylogenetic trees from genbank files

Workflow for identifying and classifying homologous gene/protein sequences

An Example of Subgenome Phasing for Complex Allopolyploidy

Feature-aware Directed OrtholoG search

Tree-based orthology inference with functionality for reducing contamination

Feature-aware orthology prediction tool. Provided data package: Quest for Orthologs reference gene sets 2019.

Collection of scripts for gene age sorting and multi-omics data mining and analysis

Reproducible phylogenomics pipeline that builds partitioned species trees from BUSCO v5 results.

Research compendium for Viscardi et al, 2020.

Supplementary data and pipelines for analyzing genome gene content data and morphology to create various phylogenies.

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.

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.

Reproducible analysis of mutant-versus-control mouse RNA-seq data focused on Wnt/β-catenin, TCF/LEF, craniofacial, osteogenic, and regulatory programs, with human–mouse orthology validation, evidence-audited networks, and Docker, Nextflow, and Snakemake workflows.

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.