Genome wide orthology inference and dNdS estimation

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. 🐵

a broadly applicable tool for automated gene identification and retrieval

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

Protein orthologous group assignment with deep learning

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 ⚡

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.

Feature-aware Directed OrtholoG search

Trace intervals between genomes using a synteny map

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

Tree-based orthology inference with functionality for reducing contamination

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

Reciprocal BLAST analysis pipeline with Snakemake and Django

HybSuite is a bash script which is designed to solve phylogenomic issues via the orthologs inference pipeline (HybPiper and ParaGone) .Besides, it is a strong tool for using NGS (next generation sequences) data to construct phylogenetic trees by only one run.