Install proteinortho with Homebrew, apt

Project links

• Homepage
• Package manager page

Commands and aliases

• proteinortho
• proteinortho2html.pl
• proteinortho2tree.pl
• proteinortho2xml.pl
• proteinortho6.pl
• proteinortho_cleanupblastgraph
• proteinortho_clustering
• proteinortho_compareProteinorthoGraphs.pl
• proteinortho_do_mcl.pl
• proteinortho_extract_from_graph.pl
• proteinortho_ffadj_mcs.py
• proteinortho_formatUsearch.pl
• proteinortho_grab_proteins.pl
• proteinortho_graphMinusRemovegraph
• proteinortho_history.pl
• proteinortho_singletons.pl
• proteinortho_summary.pl

Project history

Proteinortho was developed by Marcus Lechner and collaborators to identify orthologs and co-orthologs efficiently in large collections of genomes. An early public project page documents the tool in use by 2009, and the methodology was formally published in BMC Bioinformatics in 2011.

Later development expanded search-engine support, parallel clustering, large-project handling, and the PoFF synteny extension. The maintained project documents DIAMOND as its default similarity-search backend while retaining alternatives such as BLAST and MMseqs2.

Adoption history

The original publication presented Proteinortho as a stand-alone approach designed for large comparative-genomics datasets and demonstrated it across hundreds of bacterial genomes.

The official project documentation now describes use through native command-line installation, Debian-family packages, Galaxy, and nf-core modules. It also supports several sequence-search engines, allowing the orthology workflow to fit different performance and sensitivity requirements.

How it is used

Provide at least two species-specific FASTA files. Proteinortho performs all-against-all sequence comparison, constructs a similarity graph, and emits ortholog groups plus pairwise relationship data.

Use a search-backend option to select DIAMOND, BLAST, MMseqs2, or another supported aligner. The synteny mode invokes PoFF when conserved gene order should influence ortholog discrimination.

Proteinortho writes intermediate databases and results near the working data, so the selected working directory must be writable.

Why package nerds care

Proteinortho packages a multi-stage comparative-genomics workflow—similarity searches, graph construction, and clustering—behind one command-line interface. Bioinformatics package users value its ability to resume or reuse intermediate work, scale across many species, switch search backends, and optionally incorporate conserved gene order through PoFF.

Timeline

• 2009: An early public Proteinortho implementation was available from the University of Leipzig bioinformatics group.
• 2011: The Proteinortho methodology was published in BMC Bioinformatics.
• Later development: PoFF added synteny-aware orthology analysis.
• 2023: A new methodology paper documented the modern large-scale workflow and algorithmic improvements.

Related projects

• Proteinortho orchestrates external similarity-search programs, including DIAMOND and NCBI BLAST, before clustering the resulting relationship graph. Its PoFF extension adds gene-order information to improve discrimination of orthologs.

Sources

• https://doi.org/10.1186/1471-2105-12-124
• https://gitlab.com/paulklemm_PHD/proteinortho/-/tree/master
• https://www.bioinf.uni-leipzig.de/~marcus/software/proteinortho/