Phyrex

Phyrex reconstructs ancestral gene expression profiles and nucleotide sequences on phylogenetic trees to infer evolutionary changes in continuous characters.

Key Features:

• Ancestral Reconstruction: Reconstructs ancestral gene expression profiles and ancestral nucleotide sequences to infer past states of genomes.
• Minimum Evolution Algorithm: Implements a Minimum Evolution algorithm tailored for continuous character analysis, applied to relative gene expression levels and alternative splice site usage to reconstruct ancestral states and measure evolutionary change along branches.
• Integration with BaseML and ClustalW: Combines BaseML and ClustalW for sequence reconstruction and phylogenetic analysis.

Scientific Applications:

• Comparative Genomics: Traces the evolution of biomolecular processes and enables systematic analysis of lineage-specific evolutionary changes.
• Gene Expression Analysis: Applied to primate gene expression datasets to identify transcription factor binding sites that have undergone substitution and potentially drive lineage-specific differences in gene expression.

Methodology:

Uses a Minimum Evolution algorithm for continuous character analysis to reconstruct ancestral character states and measure evolutionary changes along branches, with sequence reconstruction supported by BaseML and ClustalW.