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I have fasta file with alingned several sequences (from MUSCLE), when I open it (e.g. notepad++) they look like: enter image description here

And I want dot format of identities like enter image description here and then save it in txt file.

I failed using MEGA, BioEdit, Jalview and CodonCode, how can I do this?

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  • $\begingroup$ Hi ... this is definitely in MEGA. Could you check again? Try updating to MEGA X? $\endgroup$
    – M__
    May 27 '20 at 13:55
  • $\begingroup$ @Michael yes I tried. Export to xls and xlsx - crashed. Csv - fine, but only first 1000nt. Unfortunately I have about 40 sequences ~25kb length each. MEGA can't handle this amount of data. $\endgroup$
    – Adamm
    May 28 '20 at 5:12
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    $\begingroup$ okay, it must be done because it is very easy to code e.g. via AlignIO in Biopython ... you'll need to adapt it, but all you are doing is splicing through an alignment. $\endgroup$
    – M__
    Jun 26 '20 at 19:31
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This is a comment rather than answer - but not enough rep

I don't think you'll find any tool to do this exactly as you want - how is it going to decide what's a dot and what's a letter (or a space,N or whatever) if you have multiple ambiguities or even an even number of alignments split 50:50?

Wouldn't be hard to code something which prints the whole column if it consists of non-identical nucleotides, else dots. Would be easy in R, could probably even do it in Excel without too much effort and no need to use VBA.

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