I am trying to analyze a number of repetitive sequences and as one step want to calculate a sequence divergence between the elements I found.

Now in theory I wanted to generate a MSA of the sequences (~100bp times ~15k) and use the MEGA7 option to calculate pairwise and mean divergence. But sadly I run into the problem:

Error# 4511 encountered: No common sites were found for the sequence pair (193,4).

and my MSA I generated with MAFFT looks like:


basically my sequence normally is 95% conserved just single individuals lead to the accumulation of those gaps, I am not sure how I can reduce these.

How can I calculate the sequence divergence? Any other programs? Any other methods?

  • 3
    $\begingroup$ consider removing those sequences? It's unlikely that any numbers you obtain for them will be very meaningful. $\endgroup$ – heathobrien Jun 15 '18 at 14:05

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