HMM-kalign package consists in the HMMER-2.3.2 package supplemented with  a new function to generate sub-optimal alignments between one sequence and one HMM. developed by E. Becker, A. Cotillard in R. Guerois's lab LINKS :   - Download HMM-kalign package (includes HMMER-2.3.2 + HMM-kalign function). - Download Specific UserGuide for HMM-kalign function   - GNU General Public License   ADDITIONAL INFO : - Supplementary Data 1 : How to drive HMM Architecture using Secondary Structure Conservation ? - Supplementary Data 2 : Protein Families considered in the Testing Procedure. - Original HMMER webpage Recent development of strategies using multiple sequence alignments (MSA) or profiles to detect remote homologies between proteins has led to a significant increase in the number of proteins whose structures can be generated by comparative modelling methods. However, prediction of the optimal alignment between these highly divergent homologous proteins remains a difficult issue. We present a tool based on a generalized Viterbi algorithm that generates optimal and sub-optimal alignments between one sequence and one HMM. The tool is implemented it as a new function within the HMMER package called hmmkalign. To generate alternative alignments in the neighborhood of the OSA, one solution is to use a generalized Viterbi algorithm that precisely determines the k-best sequences of states that maximizes the emission of sequence to be aligned. This generalization of the Viterbi algorithm has been used in the field of speech recognition and elegant variants have been developed recently that fasten the process. We implemented and included the generalized Viterbi algorithm in the program HMMER.