Hello
I am new to Nextstrain and still have a lot to learn. I am working with measles sequences. Most of my samples are 15678nt long. But I have samples that have 6nt long insertions, and some indels which are all true. I would like to keep the gaps in the other sequences rather than trimming out the insertions. Are the gaps left in the aligned sequences a problem?
Thanks
Vanessa
Including gaps in your alignments should be fine. You can learn more about how Nextstrain treats gaps here. Note that gaps should be reported as ā-ā characters in the alignment, rather than āNā characters.
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