EqualTDRL

EqualTDRL enumerates all equivalent parsimonious tandem duplication random loss (TDRL) rearrangement scenarios between two mitochondrial gene orders, focusing on cases where one order can be transformed into the other by a single TDRL event.

Key Features:

• Comprehensive Analysis: Produces the complete set of parsimonious TDRL events that could explain differences between two mitochondrial gene orders.
• Visualization: Generates visual representations of gene order rearrangements using the ggplot2 package in R.
• Implementation: Implemented in C++ for computational efficiency.

Scientific Applications:

• Evolutionary reconstruction: Infers equivalent parsimonious TDRL pathways to support reconstruction of mitochondrial gene order evolution.
• Comparative genomics: Identifies alternative TDRL rearrangement scenarios for comparative analysis of mitochondrial genomes.

Methodology:

Enumerates equivalent parsimonious tandem duplication random loss (TDRL) rearrangement scenarios between two mitochondrial gene orders under the assumption that one order is convertible to the other by a single TDRL; visualizes results with ggplot2 in R; implemented in C++.