MaM

MaM processes and manipulates multiple sequence alignments to compute locations of common repeat elements, exons, and unique regions for comparative and phylogenetic analyses.

Key Features:

• Location Computation: Accurately computes the exact locations of common repeat elements, exons, and unique regions within multiple genomic alignments.
• Subalignment Extraction: Extracts subalignments corresponding to identified DNA regions for independent or combined analysis.
• Segmented Graphical Displays: Generates graphical displays segmented into repeat, non-repeat, and coding portions to assess sequence variation across regions.
• Phylogenetic Analysis Support: Enables processing of specific alignment portions to facilitate phylogenetic analyses of sequences.
• Integration with External Resources: Utilizes user-specified programs, databases, and tables to tailor analyses.

Scientific Applications:

• Phylogenetics: Supports phylogenetic inference by isolating and analyzing coding and non-coding subalignments.
• Comparative Genomics: Enables comparison of conserved and variable regions across genomes using computed repeat, exon, and unique-region locations.
• Evolutionary Biology: Facilitates investigation of sequence variation and the evolution of structural genomic elements.

Methodology:

Processes multiple sequence alignments to compute locations of repeat elements, exons, and unique regions, extract corresponding subalignments, and generate segmented graphical displays using user-specified programs, databases, and tables.