ecceTERA

ecceTERA resolves non-binary gene trees by reconciling gene histories with species trees to infer horizontal gene transfers, duplications, and losses.

Key Features:

• Resolution of Non-Binary Gene Trees: It resolves poorly supported branches in gene trees reconstructed from sequence alignments by refining collapsed non-binary nodes.
• Integration with Species Trees: It leverages species-tree information to guide resolution and reconstruction of gene gain and loss events.
• Handling Complex Gene Events: It models horizontal gene transfer alongside gene duplication and loss when reconstructing gene histories.
• Algorithmic Efficiency: It uses an exact parameterized algorithm that resolves non-binary trees in single-exponential time by parameterizing on the number of connected low-support branches or the maximum number of children after collapsing.
• Optimal Solution Guarantee: It guarantees optimal solutions under its reconciliation cost model and reports exponential improvements over previous algorithms in computational time and accuracy.
• Solution Selection Framework: It provides a framework to select among multiple optimal solutions based on available data.

Scientific Applications:

• Comparative Genomics: It supports comparative genomics analyses that require resolved gene histories across species.
• Evolutionary Biology: It enables evolutionary biology studies of gene family evolution involving transfers, duplications, and losses.
• Molecular Evolution: It aids molecular evolution investigations dependent on accurate gene tree topologies.
• Benchmarking and Evaluation: It has been tested on simulated and biological datasets, producing results comparable in quality to other methods while reducing computational time.

Methodology:

Unsupported branches are contracted into non-binary nodes (polytomies) and then resolved by reconciling gene trees with species trees while considering horizontal gene transfers, duplications, and losses using an exact parameterized algorithm that runs in single-exponential time parameterized by the number of connected low-support branches or the maximum number of children after collapsing.