Genome wide orthology inference and dNdS estimation

a broadly applicable tool for automated gene identification and retrieval

Taxon-aware analysis of clustered protein sequences

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

Protein orthologous group assignment with deep learning

A high performance tool to identify orthologs and paralogs across genomes.

rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

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

Find reciprocal best hits (DIAMOND or BLAST) between two (or more!) sets of sequences.

Feature-aware Directed OrtholoG search

Use Thor's Axe to cut exons into their evolutionary building blocks ⚡

scripts to process, join, split, or add new proteins to a supermatrix alignment using hmms

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

Trace intervals between genomes using a synteny map

Tree-based orthology inference with functionality for reducing contamination

A shell script that uses diamond to compute the reciprocal best hits between two proteomes in a rush.

Algorithm to infer clusters of isoorthologous transcripts using gene-level homology relationships and a Reciprocal Best Hits approach

A snakemake workflow for the OrthoEvol python package.

A stand-alone tool for evaluating simple statistics of orthologs

Dynamic core orthologs compilation tool