In all the mentioned tools, when the input is a fasta file with amino acids (protein), then the output will have two added hashtag lines (##) and therefore becomes formally an "ali" file.
This does not happen with nucleotide input files.
It should be fixed so that if the input is fasta without hashtags, also the output is fasta without hashtags, both for nucleotide and protein sequences.
In all the mentioned tools, when the input is a fasta file with amino acids (protein), then the output will have two added hashtag lines (##) and therefore becomes formally an "ali" file. This does not happen with nucleotide input files. It should be fixed so that if the input is fasta without hashtags, also the output is fasta without hashtags, both for nucleotide and protein sequences.