Phylo-mLogo

Phylo-mLogo visualizes large multiple sequence alignments as global and clade-specific sequence logos to reveal conservation, variability, and clade-specific amino-acid changes for studies of viral evolution, epidemic tracing, and gene family analysis.

Key Features:

• Global and Local Visualization: Generates global logo patterns across entire multiple sequence alignments and hierarchical homologous logos specific to each clade.
• Variability and Homogeneity Analysis: Calculates variability and homogeneity within alignments using base frequencies or entropy measures to assess conservation and variation.
• Site-focused Analysis: Enables concentration on structurally or functionally constrained sites that can be selected manually or identified automatically by built-in calculations.
• Hierarchical and Symbolic Visualization of Large Datasets: Produces symbolic, hierarchical visualizations suitable for simultaneous analysis of hundreds or thousands of aligned sequences and for examining amino-acid site changes across homologous/orthologous and influenza virus sequences.

Scientific Applications:

• Phylogenetic and Epidemiological Reconstruction: Supports reconstruction of epidemiological histories and phylogenies from large sequence datasets.
• Viral Evolution Studies: Facilitates analysis of viral evolution and dynamics in epidemic or influenza virus datasets.
• Gene Family and Homology Analysis: Assists investigation of gene family dynamics and conserved versus variable sites across homologs and orthologs.
• Functional Site Mapping: Enables examination of amino-acid site changes and mapping of structurally or functionally constrained positions.

Methodology:

Produces sequence logos from multiple sequence alignments at global and clade-specific levels, computes variability and homogeneity using base frequencies or entropy measures, and allows site selection either manually or via built-in automatic identification.