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

Dynamic core orthologs compilation tool

💻 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).