A creation of multiple alignments representing structural homology and evolutionary homology, require separate approaches. PRANK is designed for construction of multiple alignments reflecting the evolutionary homology and phylogenetic information to handle insertions and deletions.
Sequence analysis
Löytynoja A "Phylogeny-aware alignment with PRANK." Methods Mol. Biol. 2014;1079 https://doi.org/10.1007/978-1-62703-646-7_10
PMID: 24170401
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