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

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

Tree-based orthology inference with functionality for reducing contamination

Research compendium for Viscardi et al, 2020.

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

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

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.

A stand-alone tool for evaluating simple statistics of orthologs

orthology_map is a pipeline designed to integrate suite of orthology assignment tools to contribute in a consensus based scoring algorithm

The Docker integration for the r2g project.

Java code to download genomes and orthologues from Ensembl

A Bio2BEL package for the terminology from FlyBase (http://flybase.org/)

💻 Archive of my bioinformatics tool for exploring evolutionarily conserved 🧬 proteins across five model organisms using orthology databases (eggNOG, inParanoid, Homologene etc.). 🎓 Part of my PhD project, King's College London (2013-2019).

💻 Archive of my bioinformatics tool for exploring evolutionarily conserved 🧬 proteins across model organisms using Gene Ontology annotation extension. 🎓 Part of my PhD project, King's College London (2013-2019).

A Bio2BEL package for converting the Mouse Genome Informatics Database (MGI) to BEL

A Bio2BEL package for converting Entrez and HomoloGene to BEL

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.

Static, client-side Fusarium gene analysis tool: ortholog mapping, PPI networks, phylogenetic trees, and GO/KEGG enrichment across 20 species — no backend required.

A web application for evolutionary rooting of genes

Orthologs Databases — Archive of bioinformatics databases and PHP processing pipelines for cross-species ortholog analysis across 7 model organisms (2012-2016). Integrates data from 21 sources including HomoloGene, InParanoid, OrthoMCL, eggNOG, BioGRID, STRING, Gene Ontology, KEGG, and Reactome.