FDSTools would sometimes produce suboptimal alignments. Most notably, it
it would produce multiple smaller insertions/deletions when the
difference between two sequences could be described by one larger
insertion/deletion in combination with a base substitution. The latter
description is often more biologically sound and also usually results in
a shorter allele name.
* Fixed a bug that sometimes caused FDSTools to choose an incorrect path
through the alignment matrix, producing a suboptimal alignment.
* Tweaked the alignment parameters to produce more meaningful results.