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Integrating different alignment strategies, a layout editor and tools deriving phylogenetic trees in a 'multiple alignment environment' helps to investigate and enhance results of multiple sequence alignment by hand. QAlign combines algorithms for fast progressive and accurate simultaneous multiple alignment with a versatile editor and a dynamic phylogenetic analysis in a convenient graphical user interface. Availability: QAlign is freely available over the internet atdoi:10.1093/bioinformatics/btg197 pmid:12912847 fatcat:622zfla6qrcx3i2iay5m45aqrq