Clustal Omega - 1.2.4
I align about 600 (n) highly identical sequences. n-1 sequences are identical. There is one sequence which has some differences. For some regions I get an alignment which is obviously suboptiomal (gap is one base to early).
EDIT: This is just one example. Obviously I could just correct this manually. But I automate a process where such alignments should not happen.
ClustalO call is the following:
clustalo -i inp.fasta -o out.clo -t DNA --outfmt=clu --full --dealign --auto
I get the following suboptimal alignment (just a small part not showing all the n-1 identical sequences):
CTCAAGTAACTTCTTTT CTCAAGTAACTTCTTTT CTCAAGTAACTTCTTTT CTCAAGTAACTTCTTTT CTCAAGTA-ACTTCTTT ******** * ***
How can I:
- Optimize the aligment with ClustalO?
- Do a post-optimization?
- Or do I have to use a different aligner? For mostly highly identical sequences.