Genome wide orthology inference and dNdS estimation

Taxon-aware analysis of clustered protein sequences

a broadly applicable tool for automated gene identification and retrieval

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

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

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

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.

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

Feature-aware Directed OrtholoG search

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.

A snakemake workflow for the OrthoEvol python package.

A stand-alone tool for evaluating simple statistics of orthologs

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

Dynamic core orthologs compilation tool