How to change sequence format in my alignment file?

Question

[Adam]

Hello,

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

And I want dot format of identities like

and then save it in txt file.

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

[GenoMax]

Have you tried Jalview (LINK)?

[Adam]

Yes, I installed it and it does't even start...

[GenoMax]

If you are not able to install try one of the older versions that used webstart.

[Adam]

Thanks, i got it. But I'm still undable to save it (dots instead of nucleotides)

[GenoMax]

Please use these directions: How to add images to a Biostars post

[Friederike]

I failed using MEGA, BioEdit and CodonCode

What issues were you running into? Did the tools not run at all or did the results not look like what you had hoped for?

[Adam]

MEGA crashed during export (xls, xlsx). Csv went fine but only 1kb have been exported. I have alignment of 40 sequences, ~25kb each. BioEdit - I was abe to change letters to dots, but each export always contained letters. CodonCode - here I exported what I want but only positions with changes.

[Friederike]

CodonCode - here I exported what I want but only positions with changes.

Isn't that what you wanted?

[Adam]

I was looking for full sequences but I'll be content with this result