TranslatorX is a tool to align (protein-coding) nucleotide sequences based on the corresponding amino acid alignments. Given a set of nucleotide sequences, TranslatorX translates them to amino acids using the appropriate genetic code, aligns those amino acid sequences and, from the resulting alignment, determines the optimal alignment of nucleotide sequences.
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Abascal F, Zardoya R, Telford MJ (2010)
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations
Nucleic Acids Res. 38:W7-13.