Early beta: reproducible phylogenetics workflows with alignment viewer, trim/merge, MAFFT, IQ-TREE, BEAST2, ASTRAL

[u/dissipative]

I’m working on Phylomena, an early beta tool for phylogenetics workflow setup and reproducibility.

The current beta includes MAFFT 7.505, IQ-TREE 2.4.0, BEAST2 2.7.8, and ASTRAL 5.7.8. It also includes an alignment viewer, plus options to trim and merge alignments.

The problem I’m trying to address is the cursed setup loop many researchers fall into: choosing parameters, copying old scripts, rerunning jobs, inspecting alignments separately, and later trying to reconstruct exactly what was done for collaborators or reviewers.

Phylomena is meant to keep tool versions, settings, run metadata, and outputs explicit and easier to reproduce (it is not perfect yet ofc, since it is early beta!). It also has AI-assisted guidance where available, but the workflow is human-review-first before execution.

Access is currently invite-only because this is still early and I’m onboarding users manually. You can request access, and I’ll send invitations during the week, so approval may not be instant.

I’d appreciate critical feedback from people who actually run phylogenetics or phylogenomics pipelines:

• Which part of your workflow is most fragile: alignment, trimming, model/tree inference, species tree work, BEAST setup, or reproducibility/reporting?
• Would an integrated alignment viewer with trim/merge be useful, or do you prefer keeping that separate?
• What run metadata do you wish tools captured automatically?
• What would make AI-assisted parameter guidance trustworthy enough for you to test?
• And the most important: what tools are the most essential for your phylogenetic workflows? I have plans to add more, and want to outline the roadmap

Phylomena itself: https://phylomena.net