[BioRuby] Alignment plugin

[Matt]

> Each nucleotide/aminoacid has properties by itself. Do gaps have
> properties?
>

Not sure if you mean a single gap ("-") or any gap between
nucleotides.  If the latter then it would be nice if gaps had
properties like

* length
* at_beginning_sequence (preceeds all bases)
* at_end_of_sequence    (found at end of all bases)

Another distinction- gaps in found in a typical MSA may indicate real
gaps (as inferred from evolutionary events in an alignment), or
missing data, depending on how sloppy/precise a person is.

cheers,
Matt