domains / families / science / gene-tree-species-tree-reconciliation

gene-tree-species-tree-reconciliation

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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 DL+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.

When to use

• inferring ancestral gene-family content
• distinguishing duplication from horizontal transfer from differential loss
• rooting deep species trees from gene-content signals
• counting DTL events per branch
• refining noisy gene trees against a species tree
• modeling WGD events jointly with DTL
• producing publication-grade gene-family histories

When not to use

• tasks not stated in the skill text

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