What are the pros and cons of using in-frame nucleotide sequence alignments
comapred with using non in-frame nucleotide alignments for making
For example, I have some sequences with indels, but with conserved motifs
at either end. Using Megalign (Lasergene) I can make an amino acid
alignment and then convert it to the equivalent nucleotide alignment,
export it and use DNAdist (Phylip) to work out the rate of change
at each codon position, and then use those parameters in DNAdist
again to give a distance matrix for Neighbor.
Alternatively, I can align the nucleotide sequences with e.g. Clustal,
perhaps using the treefile from the above analysis as a guide tree,
to give an input dataset for DNAdist, and then go to Neighbor.
The alignments made by these two methods are similar, but not the same.
If the non in-frame alignment has more aligned postions (columns) is
it 'better' than the in-frame alignment, which could be argued to be
more biologically 'real'?
(As an aside, are there any public domain alignment programs that can
make in-frame alignments as the commercial Megalign does?)
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