EndoRex

EndoRex reconciles gene trees with species trees to model gene family evolution through duplication, loss, and endosymbiotic gene transfer (EGT) between mitochondrial and nuclear genomes.

Key Features:

• Endosymbiotic Gene Transfer (EGT) Analysis: Models EGT as a special case of horizontal gene transfer between mitochondrial and nuclear genomes and distinguishes EGTcopy (retained source copy) and EGTcut (removed source copy).
• DLE Distance Computation: Computes the DLE (Duplication, Loss, and EGT) distance using a linear-time algorithm.
• Dynamic Programming Enumeration: Uses dynamic programming to enumerate all optimal reconciliations for arbitrary operation cost settings.
• Optimal Reconciled Trees: Produces optimal reconciled gene trees integrating gene family events with species phylogeny.

Scientific Applications:

• Eukaryotic Genome Evolution: Reconstructs histories of duplication, loss, and EGT to study the evolution of eukaryotic genomes.
• Plant Mitochondrial–Nuclear Repertoire Analysis: Analyzes variability in gene repertoires between nuclear and mitochondrial genomes in lineages such as land plants.
• Rooting Eukaryotic Phylogeny: Provides modeled evidence of organelle-to-nucleus transfers relevant to rooting the eukaryotic tree.

Methodology:

Infers gene-family histories via duplication, loss, and EGT; computes DLE distances with a linear-time algorithm; and reconciles gene trees with species trees using dynamic programming to enumerate all optimal reconciliations under arbitrary cost settings.