GenePainter

GenePainter maps gene structures onto protein multiple sequence alignments and integrates conserved intron positions, including intron phase, into phylogenetic analyses to support reconstruction of gene family evolution.

Key Features:

• Intron-Phase Alignment: Maps intron positions onto protein MSAs while preserving intron phase and nucleotide-level alignment.
• Large Dataset Management: Processes extensive datasets and permits selection of specific subsets for targeted analysis.
• Exhaustive Statistical Analysis: Produces comprehensive statistical outputs to support phylogenetic inference.
• Integration with Phylogenetic Trees: Incorporates exon–intron pattern conservation directly into phylogenetic trees to assist in resolving subfamily relationships and inferring gene family histories.
• Versatile Output Formats: Exports results in plain-text and graphical formats for downstream analysis and visualization.

Scientific Applications:

• Evolutionary and Genomic Analysis: Studying the evolution of eukaryotic gene families using conserved intron positions.
• Phylogenetic Reconstruction: Reconstructing phylogenetic trees by mapping conserved intron positions onto MSAs.
• Subfamily Resolution: Resolving ambiguous relationships within protein subfamilies through exon–intron pattern conservation.
• Gene Family History Inference: Inferring gene family histories from conserved exon–intron architectures.

Methodology:

Aligns gene structures to protein MSAs at nucleotide resolution while retaining intron positions and phases, and maps exon–intron pattern conservation onto phylogenetic trees.