Opsin evolution: alignment

This shows an alignment of 157 opsins, almost all of ciliary type. It needs some trimming of unalignable ends to fit better. Fragmentary sequences of course score low and so fall to the bottom -- that's still useful because these fragments represent two important clades, jawless fish and chondrichthyes. Notice the numerous invariant (blue) and nearly invariant sequences (red) -- these anchor the alignment with near-certainty. Opsins have seven alpha helical sections traversing the cell membrane with the intervening sequence alternating as cytoplasmic and extra-cellular. Among other things, the alignment shows that the opsin classifier has properly named the opsins -- each ortholog classifies together as expected from its name. Deletions and insertions show up clearly on the alignment and are readily resolved as to type using the phylogenetic ordering to establish ancestral conditon.