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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:

>h1
-------gat-tt------------tgta--t---c-t------a---ta---t--t-a-
g-ca--tt-c-tt-t--at----------c----------a--------------ttt--
--------a---t-aata----------c---------c-------------------t-
------ag-a--a-a--------------------t-------------g----------
----t------tt-t-a-a---aa------------------------------------
------t--g--------c-----a-a-t-----t-----t-------------------
-------------a-------a--a--c---c-----a---t-t------------tt--
------------------t---g---g---------t------------------t-t--
---t-----g-a--tc--------------------at-------a--gt-ag----gc-
---t------a---t--t------t-t---c--a--a----a---a--aaatatc---

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?

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    $\begingroup$ consider removing those sequences? It's unlikely that any numbers you obtain for them will be very meaningful. $\endgroup$
    – heathobrien
    Commented Jun 15, 2018 at 14:05

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