Sequencing Data
DNADynamo will open and align sequencing data. Most .abi and .scf sequencing data file formats are supported. You can also open and align plain sequences in fasta format files or flat txt files.
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Sequences are either aligned to a reference/guide sequence for comparison to an expected result/mutation analysis or assembled into a new contig/consensus sequence.
Sequence and alignment editing is performed using the 'editing buttons', mouse select and drag, or typing on the keyboard (replacement bases or keyboard shortcuts).
Sequence alignments (and translations) are shown in the upper display area while the lower display shows traces, maps, translations or an alignment and mutation summary.
Mismatches in the alignments are highlighted in the sequence and on an 'overview' graphic map illustrating the alignments and mismatches.

To align sequences to a reference/guide sequence, start from a DNADynamo window that contains the reference sequence, and use menu option 'Sequencing' -> 'Open and align sequencing data to this windows sequence'. A file chooser will open, from which you can select multiple sequence files to align to the reference/guide sequence.
To align sequencing data to form a new contig/consensus, start from an empty DNADynamo window, and use menu option 'Sequencing' -> 'Open and assemble sequence data files to form a new contig'.
You can also use the 'File Manager' to select multiple sequencing files for alignment. You can set one of the selected files as the reference/guide
Relationship between the 'standard' DNA sequence window and the 'alignment editor' window
When you align sequences to a reference/guide sequence in a standard window, the alignment is part of that guide/reference sequence file. From the alignment editor, you can switch back to the standard window by pressing the 'standard window' button. From the standard window, you can switch back to the alignment by pressing the 'alignment data' button. Consequently you can only associate one alignment with a certain DNADynamo standard window and file. If you want to align other sequences in a separate project, you need to duplicate the original file, or copy and paste the reference sequence into a new empty window, and align from there.
When the sequences are aligned to form a new contig, pressing the 'standard window' button takes you to the standard window where the sequence is the consensus of the alignment. Pressing the 'alignment data' button takes you back to the 'alignment editor'