comparative-genomics-gene-tree-species-tree-reconciliation

comparative-genomics-gene-tree-species-tree-reconciliation is a Bioinformatics & life sciences skill for AI agents, published by swaruplab in the operon repository on GitHub. Skillspace rates comparative-genomics-gene-tree-species-tree-reconciliation C (79/100) and it passed the safety scan; the rating is based on static analysis only.

Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DTL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

Grade

C

Quality

79 / 100

Safety

Passed

GitHub stars

90

Unproven: rated by static analysis only, not yet compared head-to-head.

Not launch-quality. It is graded C with a clean safety verdict, but our quality filters exclude it: it is a near-duplicate variant of another skill. So it is not in our launch-quality set, the skills our MCP server searches and recommends. How launch-quality is decided

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