by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. 1 Sequence Analysis Upcoming Challenges for Multiple Sequence Alignment Methods in the High-Throughpu

This review focuses on recent trends in multiple sequence alignment tools. It describes the latest algorithmic improvements including the extension of consistency based methods to the problem of template based multiple sequence alignments. Some results are presented suggesting that template based methods are significantly more ac-curate than simpler alternative methods. The validation of existing methods is also discussed at length with the detailed description of recent results and some suggestions for future validation strategies. The last part of the review addresses future challenges for multiple sequence alignment methods in the genomic era, most notably the need to cope with very large sequences, the need to integrate large amounts of experimental data, the need to accurately align non-coding and non-transcribed sequences and finally, the need to inte-grate many alternative methods and approaches. Contact