Gene to Reference Tree

Build a protein gene tree through explicit, reviewable decisions. Treat database acquisition, reference sampling, alignment, rooting, and literature comparison as scientific analyses rather than mechanical top-hit processing.

Preserve the core claim

• Call the result a gene tree, not a species tree.
• Treat similarity as evidence of homology, never as proof of orthology or identical function.
• Treat support as repeatability under a method, not proof that the topology is correct.
• Preserve the raw candidate pool, untrimmed alignment, unrooted tree, commands, versions, database snapshots, and every exclusion.
• Never upload an unpublished sequence, candidate set, tree, or metadata to a remote service without explicit permission.

Run the workflow

1. Classify and resolve the query

Classify the input as: