Multiple alignment and editor using DCA, CLUSTAL-W, T-COFFEE, and DIALIGN. QAlign provides a practical solution for the creation of high-quality multiple alignments: layouts produced by automated methods may be used as a starting-point for manual changes, whereas the phylogenetic consequences are visualized on the fly. The standalone software package combines various alignment algorithms with a versatile editor and a dynamic phylogenetic analysis to provide a convenient graphical user interface. In addition to the traditional alignment strategies of fast progressive (Clustal W) and more accurate simultaneous multiple alignment (DCA), QAlign includes iterative and consistency-based state-of-the-art extensions, which recently have shown much promise (T-coffee and DIALIGN). Thus, after providing the input sequences (FASTA and MSF format) and selecting the evolutionary model (PAM, BLOSUM, DNA/RNA), the user may choose from a list of strategies/algorithms that one which suits the problem best. However, even these layouts may need some manual editing. Therefore, the graphical editor of QAlign provides all features needed to support convenient editing. A dynamical consensus is updated on every edit event, visualizing the strength of each character in an easy coloring scheme. Furthermore, a phylogenetic analysis of the current alignment layout is created interactively (using the neighbor-joining method), which may be refined (e.g. by applying bootstrapping techniques) and exported (NEWICK and SVG or WMF vector-format)
