Alignancer is a tool for alignment enhancing. It is performing additional alignments on masked sections of hmmalign (HMMER 3.0) multiple alignments. ClustalW (default) or Muscle is being utilized to automatically align all sections which were not covered by a profile HMM and therefore were not aligned. In using additional aligners to complement hmmalign, compulsory loss of information may be avoided keeping the entire alignment for subsequent analyses, e.g. the calculation of phylogenetic trees.