T-REX

T-REX reconstructs phylogenetic trees, reticulograms, and infers horizontal gene transfer (HGT) events to analyze complex evolutionary relationships.

Key Features:

• Phylogenetic Tree Reconstruction: Supports multiple alignment and tree-building methods including MUSCLE, MAFFT, Neighbor Joining, NINJA, BioNJ, PhyML, RAxML, and includes a random phylogenetic tree generator.
• Reticulation Networks: Implements algorithms for reconstructing reticulograms to represent hybridization and recombination events.
• Horizontal Gene Transfer Inference: Detects and validates complete and partial gene transfers, infers consensus HGT scenarios, and identifies HGT events.
• Distance Matrix Analysis: Infers phylogenetic trees from both complete and incomplete distance matrices.
• Sequence-to-Distance Transformation Models: Incorporates models for transforming sequence data into distance matrices for downstream analysis.
• Validation and Visualization: Provides validation and visualization of phylogenetic trees and networks derived from distance or sequence data.

Scientific Applications:

• Evolutionary relationship inference: Reconstruction of genetic relationships among organisms using trees and networks.
• Hybridization and recombination analysis: Resolving complex evolutionary histories involving hybrid species, recombination, or reticulation.
• Horizontal gene transfer studies: Characterization and validation of HGT events across species.

Methodology:

Multiple sequence alignment with MUSCLE and MAFFT; tree reconstruction using Neighbor Joining, NINJA, BioNJ, PhyML, and RAxML; random tree generation; reticulogram reconstruction algorithms; tree inference from complete and incomplete distance matrices; sequence-to-distance transformation models; detection and validation of complete and partial gene transfers; inference of consensus HGT scenarios.