The ability of the program POY, implementing optimization alignment, to deal with major indels is explored and discussed in connection with a phylogenetic analysis of the genus Secale based on partial Adh1 sequences. The Adh1 sequences used span exon 2-4. Nearly all variation is found in intron 2 and intron 3, which form the basis for the phylogenetic analyses. Both in some ingroup and outgroup taxa intron 3 has a major duplication. Previous phylogenetic analyses have repeatedly confirmed monophyly of both Secale and Hordeum, the latter being part of the outgroup. However, optimization alignment only recovers both genera as monophyletic when knowledge of the duplication is incorporated in the analysis. The phylogenetic relationships within Secale are not clearly resolved. Subspecific taxa of Secale strictum have identical sequences and they are confined to a monophyletic group. However, the two subspecific taxa of Secale cereale do not form a monophyletic group, and the position of Secale sylvestre is uncertain.