We present a new probabilistic model of the evolution of RNA-, DNA-, or protein-like sequences and a software tool, Rose, that implements this model. Guided by an evolutionary tree, a family of related sequences is created from a common ancestor sequence by insertion, deletion and substitution of characters. During this artificial evolutionary process, the true history is logged and the correct multiple sequence alignment is created simultaneously. The model also allows for varying rates of mutation within the sequences, making it possible to establish so-called sequence motifs.