I'm trying to use Macclade for making sequence alignments using DNA
sequences in Clustal DNA/RNA format. I though Macclade will perform an
amino acids alignment for these DNA sequences, but I was surprised that
its is respecting the codons and putting gaps in some of them (spilling
them). What can I do to avoid, or at least minimize, this problem?
It seems to me that Macclade is making a nucleotide alignment, and my
other question is, if it is possible, how can I make amino acid
alignments from DNA sequences in Clustal DNA/RNA format?
Thanks a lot