OrthoGather 2.0

A big update focused on making OrthoGather effortless to install and keeping its data fresh.

✨ Highlights

• One-click installers for macOS and Windows — no terminal, no setup knowledge. Download the file for your computer (below), double-click, and it installs everything: Python 3.11, OrthoFinder, and a Desktop app with the OrthoGather logo.
• Refreshed UniProt catalogue — 1,013,422 proteomes (UniProt release 2026_01) covering 161,743 species, with up-to-date EBI GOA links and per-proteome / per-GOA version stamps. The app checks for and applies catalogue updates automatically.
• No more Git LFS — the catalogue ships compressed (~20 MB) and unpacks itself on first launch. A plain git clone just works.
• Faster species picker — the 1-million-proteome catalogue loads ~20× lighter over the wire and search stays instant.
• Leaner install — removed unused dependencies.

⬇️ Install

• macOS (Apple Silicon & Intel): download Install OrthoGather.command, then right-click → Open.
• Windows 10/11: download Install OrthoGather.bat and double-click (it sets up WSL automatically; needs admin + one restart).

A friendly step-by-step guide is in installers/How to install OrthoGather.html in the repo.

The Windows installer is new in this release — feedback welcome via the issue tracker.

Requirements: ~3 GB free space on macOS/Linux, ~5 GB on Windows (incl. WSL); 8 GB RAM recommended.

Proteome catalogue 2026-06-03

UniProt proteome catalogue (release 2026_01, all tiers) with refreshed EBI GOA links and per-proteome/per-GOA version stamps. Ships compressed (proteomes_list.json.gz, ~20 MB); OrthoGather decompresses it on first launch and auto-updates from this asset. 1,013,422 proteomes · 161,743 species · 34,305 reference.

Orthogather v1.1.2

Bioinformatics Submission Version
This release corresponds to the version of OrthoGather submitted to Bioinformatics.

New in this version:

• Added fully reproducible example analysis (example_analysis/)
• Included input dataset (foreground/background) and complete output files
• Added dedicated README for reproducibility documentation
• Minor documentation refinements

OrthoGather v1.1.1

This release introduces important code improvements and includes a permanent
CITATION.cff file to ensure correct authorship and citation information.

OrthoGather 1.0.1

v1.0.1

Fix UpSet Excel output: numbered sheets and deterministic ordering

OrthoGather v1.0.0

GNU General Public License v3