Improved sequence aligment (variant calling) quality
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.