After beginning an alignment, an error message will appear if the sequences are not of the appropriate type or are too long for the selected algorithm. If performing a MUSCLE or Clustal Omega alignment, an error message usually indicates that the sequences are too long or that multi-segment sequence groups are ordered incorrectly. To remedy the situation, you can align using Mauve, or correctly re-enter any incorrect multi-segment sequences, or break up the sequences into shorter lengths. This last task can be performed very quickly and easily using DNASTAR SeqNinja.
During a multiple sequence alignment, you may receive the following warning:
To reveal more information, click on the Details button.
For additional details, select View > Console from the menu. An example console is shown below:
Notice that in this console, the message “Fatal error, exception caught” appears near the bottom. Either that message or an “Out of memory” message are known to occur with particularly long, highly divergent sequences.
Before attempting the alignment again, we recommend using Align > Align with Options and checking the box next to Use Brenner’s Alignment. Checking the box causes MegAlign Pro to use Brenner’s method for the root alignment. This method uses less memory, and enables the alignment of long and divergent sequences, but with a concurrent loss in accuracy.
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