A web-based tool for multiple sequence alignment (MSA) of DNA. The algorithm uses PFAM or profiles provided by a user. The web interface requires registration and login.
Phylogeny; Sequence analysis; Nucleic acid sites, features and motifs; Nucleic acid structure analysis; Sequence sites, features and motifs
Balech B, Monaco A, Perniola M, Santamaria M, Donvito G, Vicario S, Maggi G, Pesole G "DNA Multiple Sequence Alignment Guided by Protein Domains: The MSA-PAD 2.0 Method." Methods Mol Biol. 2018;1746:173-180. https://doi.org/10.1007/978-1-4939-7683-6_13
Balech B, Vicario S, Donvito G, Monaco A, Notarangelo P, Pesole G "SA-PAD: DNA multiple sequence alignment framework based on PFAM accessed domain information." Bioinformatics. 2015 Aug 1;31(15):2571-3. https://doi.org/10.1093/bioinformatics/btv141
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