CodonCode Aligner Forum

After adding sequences to an assembly with the preferences set to long gap alignment, oftentimes parts of the sequences are then grayed out, such that they are basically illegible. I can't figure out how to reverse this, its automatic and once it has happened removing the sequence from the assembly doesn't reverse it.

Greyed out parts of sequences could not be aligned - they are unaligned ends. Some possible reasons why this can happen are trying to assemble sequences that are too diverse, and low-quality / high error rate sequence at the beginning and/or end of sequences.

For individual sequences, you can use the "Mark start alignment" and "Mark end alignment" menu items (check the Aligner Help for more details). But note that this will not add any require gaps, so the formerly greyed out parts will still be misaligned.

To reduce unaligned ends, here are some things to try:
- end clip sequences before assembly
- change the scoring in the preferences, for example by reducing penalties
- make sure to use the most current version of CodonCode Aligner.