![]() View sequences in nucleotide or protein mode in protein mode, Blixem will display the three-frame translation of the reference sequence.View alignments against both strands of the reference sequence.Detail section showing the actual alignment of protein or nucleotide sequences to the genomic DNA sequence.Overview section showing the positions of genes and alignments around the alignment window.Linux – Ubuntu 14.04 (64-bit) – primary supported architecture.It should also work on several other platforms, as listed below, but is less thoroughly supported. It is also tested frequently on Mac OS X. SeqTools is well tested and in daily use on this architecture. Our primary supported platform is Ubuntu 14.04 (64-bit). Belvu is a multiple sequence alignment viewer and phylogenetic tool with an extensive set of user-configurable modes to color residues. Dotter is a graphical dot-matrix program for detailed comparison of two sequences. For more information, watch the tutorial movies about comparing contigs and round trip editing.Blixem is an interactive browser of sequence alignments that have been stacked up in a “master-slave” multiple alignment it is not a ‘true’ multiple alignment but a ‘one-to-many’ alignment. CodonCode Aligner will automatically update the gap placements, and retain the connection to the underlying sequence chromatograms.Īn screen shot that illustrates contig alignments is shown below. For difficult alignments that require a lot of manual gap adjustment, CodonCode Aligner supports round trip editing: export your aligned sequences, edit in you favorite editor like Se-Al or BioEdit, and re-import the results. You can edit your contig alignment right in CodonCode Aligner. If necessary, CodonCode Aligner will reverse-complement contigs before alignment.Choose between the standard multiple sequence alignment programs MUSCLE and ClustalW, or use the built-in algorithms to control parameters like minimum percent identity.Updates in the other views will be done automatically. Just one linked copy of your data means you can edit anywhere - in the sequence traces, the consensus sequence, or the alignment of contigs.Go back to the sequence traces with a simple double-click. ![]() Align your contig sequences directly in CodonCode Aligner, while keeping the relation to the underlying sequence traces intact (to align sequences and contigs, select the sequences and contigs, then choose "Compare contigs" from the "Advanced Assembly" in the "Contig" menu).To verify any differences, you then have to work with two separate copies of your sequence data.ĬodonCode Aligner can greatly simplify this step: 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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