  Alignment of large genomic sequences is a fundamental task in computational
genome analysis. Most methods for genomic alignment use high-scoring local
alignments as {\em anchor points} to reduce the search space of the alignment
procedure. Speed and quality of these methods therefore depend on the
underlying anchor points. Herein, we propose to use {\em Filtered Spaced Word
Matches} to calculate anchor points for genome alignment. To evaluate this
approach, we used these anchor points in the the widely used alignment pipeline
{\em Mugsy}. For distantly related sequence sets, we could substantially
improve the quality of alignments produced by {\em Mugsy}.
