When I get results from sequencing, they often overlap only partly or not at all. In such case it's easier to align them with the "parental" sequence (of what I expect), to see where they align.
However, there I must either work with each sequencing reaction separately or put it all together in a complicated way. The solution would be multiple-alignment tool, which would not try to align everything together, but rather look for maximal homology, even if it meant that in one part will be aligned two sequences and in the other part other two sequences. Is there any such tool?
Dear Tomáš,
If I understand correctly, your problem is aligning sequence reads to a reference (parental??) sequence? If so, you are not looking for a multiple sequence alignment software but for a read mapping tool.
Depending on the origin and volume of your sequence reads, different tools might be more appropriate.
Best,
Vasilis
Yeah, that's probably the correct name, although I associate that with something like RNA-Seq. Is there any such tool for low-throughput mapping? When I have only 2 or 3 sequences to be aligned to parental sequence?
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