GenePainter is a standalone tool for mapping gene structures onto protein multiple sequence alignments (MSA). Gene structures, as provided by WebScipio, are aligned with respect to the exact positions of the introns (down to nucleotide level) and intron phase. Output can be viewed in various formats, ranging from plain text to graphical output formats.
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S. Mühlhausen, M. Hellkamp & M. Kollmar (2014)
GenePainter 2.0 resolves the taxonomic distribution of intron positions.
Bioinformatics, pii: btu798
Björn Hammesfahr †, Florian Odronitz †, Stefanie Mühlhausen, Stephan Waack & Martin Kollmar (2013)
GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures.
BMC Bioinformatics 14, 77.