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A multiple sequence-alignment or (MSA) is not the same as sequence assembly so don't be surprised if your contigs and multiple-sequence alignments look different.
The ability to sequence RNA and align it prior to further analyses is a powerful but technically challenging technique. This is largely due to the fact that the powerful sequence aligners are all command-line driven.
Sequencher has several different assembly algorithms as well as different assembly modes providing the flexibility to work with any of kind sequence data.
MUSCLE
MUSCLE[2], a multiple-sequence alignment (MSA) program, joins the Sequencher 5.1 family of plugins. It joins Clustal, making it the second MSA program in Sequencher’s DNA-Seq Tools. Boasting both speed and accuracy, it compares very favorably [3] to other multiple-sequence alignment programs.
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