apex

apex provides R classes and functions to store, manage, visualize, and analyze multi-gene DNA and amino acid sequence datasets to assess phylogenetic relationships and detect phylogenetic incongruence across viruses, bacteria, and eukaryotes.

Key Features:

• New Object Classes: Extends existing R sequence storage standards to represent DNA and amino acid sequences across multiple loci.
• Data Handling and Visualization Tools: Offers functions for organizing, visualizing, and analyzing complex multi-gene sequence datasets.
• Analysis of Phylogenetic Incongruence: Enables separate locus-level analyses to identify and explore phylogenetic incongruence.
• Integration with R Ecosystem: Provides compatibility with packages implementing distance-based, parsimony, and likelihood-based phylogenetic reconstruction methods and with phylogenetic comparative methods.

Scientific Applications:

• Multi-gene phylogenetics: Management and analysis of concatenated or locus-specific DNA and amino acid data for phylogenetic inference.
• Phylogenetic incongruence assessment: Detection and preliminary investigation of discordant gene trees across loci.
• Evolutionary studies across taxa: Comparative analyses of evolutionary relationships among viruses, bacteria, and eukaryotes using multi-locus data.
• Interoperability with reconstruction methods: Downstream use with distance-, parsimony-, and likelihood-based phylogenetic and comparative analyses.

Methodology:

Extends R sequence storage classes to handle DNA and amino acid sequences from multiple loci, enables separate locus-level analyses, and interoperates with packages implementing distance-based, parsimony, likelihood-based phylogenetic reconstruction and phylogenetic comparative methods.