When you want to compare consensus sequences, most other programs force you to either duplicate the consensus sequences, or to export the sequences for alignment with a separate outside program like Clustal. A typical use is to first assemble several sequence reads for each clone into contigs, and then align the consensus sequences for the contigs. Multiple Sequence Alignment: Align Contigs and SequencesĬodonCode Aligner lets you align sequences to each other with MUSCLE, ClustalW, or the built-in alignment methods. When ignoring the reference sequence, you can choose which character (N, X, or '-') to use in regions without coverage to simplify downstream analysis with BLAST or other tools. You can choose whether the reference sequence should be ignored when building the consensus, or used as the consensus sequence. Limit your analysis to the region you are interested in.Combine sequences into a contig even of they do not overlap.CodonCode Aligner lets you designate multiple reference sequences, and will automatically pick the best reference sequence for each sample. Align to Reference SequencesĪlign your sequences to reference sequences you designate. Alignments can be edited in CodonCode Aligner, and exported in commonly used format like NEXUS/PAUP and Phylip. Sequence Alignment with CodonCode AlignerĬodonCode Aligner supports two common uses of sequence alignments: alignments to reference sequences, and multiple sequence alignments with ClustalW, MUSCLE, or built-in alignment methods.
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