Genome wide orthology inference and dNdS estimation

a broadly applicable tool for automated gene identification and retrieval

Taxon-aware analysis of clustered protein sequences

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

Protein orthologous group assignment with deep learning

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

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

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

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.

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

A snakemake workflow for the OrthoEvol python package.

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

A stand-alone tool for evaluating simple statistics of orthologs