From this post I became aware of the paper “Alignment Uncertainty and Genomic Analysis” by Wong et al..
We learn valuable lessons, some evident and some implied. I am covering only the evident here, the implied I leave for the imagination of who’s reading the paper. To the evident lessons (conclusions):
Alignments are important for genomics studies
Some genes are more difficult to align than others
Some alignment programs align some genes better than others, while other alignment programs align other genes better than some
Most genes in an organism are under the same DNA model of substitution, hence they all have identical selective pressure, drift, migration, recombination and mutation rates
There are things you can only learn from Science.