TreSpEx

TreSpEx identifies misleading phylogenetic signals in gene and species trees to detect paralogy, long-branch attraction, saturation, and conflicts between datasets that compromise phylogenetic reconstructions.

Key Features:

• Misleading-signal detection: Detects paralogy, long-branch attraction, saturation, and conflicts between datasets within phylogenetic trees.
• Tree-based statistical tests: Applies statistical tests that leverage tree-based information such as nodal support and patristic distances (PDs).
• Parallel analysis: Performs parallel analysis of numerous trees and predefined gene partitions for large-scale studies.
• Phylogenomic scalability: Designed to handle phylogenomic datasets involving hundreds of genes.
• Implementation: Implemented in Perl.

Scientific Applications:

• Phylogenetic quality control: Identifies and flags misleading signals that can bias phylogenetic reconstructions and comparative biological studies.
• Gene-partition screening: Screens predefined gene partitions to detect problematic loci in phylogenomic datasets.
• Assessment of tree reliability: Uses nodal support and patristic-distance metrics to evaluate the reliability of inferred phylogenies.
• Detection of non-orthology artifacts: Identifies paralogy and related non-orthology issues that affect evolutionary inference.

Methodology:

Performs statistical tests on phylogenetic trees using nodal support and patristic distances (PDs) and conducts parallel analyses of multiple trees and predefined gene partitions; implemented in Perl.