ProDA is a tool that constructs local multiple sequence alignments (MSAs) by first identifying repeated homologous regions in a collection of protein sequences.
Sequence analysis; Protein structure analysis; Protein folds and structural domains
Phuong TM, Do CB, Edgar RC, Batzoglou S "Multiple alignment of protein sequences with repeats and rearrangements." Nucleic Acids Res. 2006;34(20):5932-42. https://doi.org/10.1093/nar/gkl511
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