Error in MEGA x while phylogenetic analysis

Question

[jahanzaib119311]

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".

Answer 1

[gayachit]

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

Answer 2

[jahanzaib119311]

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

[gayachit]

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