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Error in MEGA x while phylogenetic analysis

while phylogenetic analysis after prope alignment with MEGA X clustal W and saving it in .meg format when I try to create ar tree it give an error "invalid base J found in line 3314".

alignment
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written by jahanzaib119311 • jahanzaib119311

2 answers

I think the error says it all. Check your file at the said position. MEGA X will not accept bases other than AUTGC or N or X for ambiguous site symbol or in case of aligned file refer https://www.megasoftware.net/web_help_10/index.htm#t=Invalid_special_symbol_in_molecular_sequences.htm

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written by gayachit gayachit

Actually I have a protein sequence can I replace it with X.

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written by jahanzaib119311 • jahanzaib119311

You could try that. However, do not replace ambiguous base with a gap it will change the scoring.

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written by gayachit gayachit

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