Laurent Guéguen

This study compares Dollo parsimony and maximum likelihood methods for ancestral gene content reconstruction, finding Dollo parsimony overestimates ancestral gene content, especially near the root of the tree.

Treerecs is a phylogenetic software that performs duplication-loss reconciliation to root gene trees and correct alignment uncertainties.

This paper clarifies how convergent adaptive evolution manifests in coding sequences, reviews detection methods, and evaluates their power through simulations.

The paper estimates synonymous and non-synonymous substitution rates while accounting for non-stationary base composition, showing that non-stationarity biases estimates and proposing methods to correct for it.