ggmsa

ggmsa visualizes multiple sequence alignments to reveal site-level conservation, variation, and recombination for analyses of gene function, evolutionary processes, and sequence–structure–function relationships.

Key Features:

• Comprehensive visualization methods: Provides sequence bundles, sequence logos, stacked sequence alignments, and comparative plots to display conservation, variation, and recombination at the site level.
• Integration with associated data: Supports combining MSA data with phenotypic data, ancestral sequences, molecular structures, functional annotations, and expression levels.
• Genome alignment visualization: Implements a method for visualizing genome alignments in multiple alignment format to explore patterns of variation within and between species.
• Scalability and ggplot2 integration: Leverages the ggplot2 framework to create scalable, composable visualizations and to combine MSA plots with ggtree, boxplots, and genome maps.

Scientific Applications:

• Molecular function analysis: Visualizing conserved and variable sites to support interpretation of gene function and sequence–structure relationships.
• Evolutionary biology: Exploring patterns of variation and recombination across species and populations for evolutionary inference.
• Phenotype and expression correlation: Relating sequence variation to phenotypic traits, ancestral states, molecular structure, and expression level data.

Methodology:

Implements sequence-level visualizations (sequence bundles, sequence logos, stacked alignments, comparative plots), a genome-alignment visualization method in multiple alignment format, and uses the ggplot2 framework for plot composition and integration with ggtree and other ggplot2 plots.