I am currently considering different multiple sequence alignment (MSA) algorithms that I could use to generate an alignment. For the comparison of different alignments (i.e. produced from different tools), I have heard it said that phylogenetic likelihoods could be used to compare different alignments. That is, one could generate different alignments, use phylogenetic software to generate a maximum likelihood value for each, and the alignment yielding the best likelihood chosen for downstream analyses.
I'm not sure if this would be valid, though. My thinking is that different tools would produce alignments of different lengths -- given differing propensities for each algorithm to force a gap -- but surely alignments of different lengths are not comparable using likelihoods, given that likelihood for the alignment represents the product (sum for log-likelihood) of all of the site likelihoods? Can anyone confirm this or add their general thoughts?