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2. MUSCLE: multiple sequence alignment with high accuracy and high throughput
3. Fletcher , W. , Yang , Z. : INDE Lible : a flexible simulator of biological sequence evolution. Molecular Biology and Evolution 26 ( 8 ), 1879 -- 1888 ( 2009 ) Fletcher, W., Yang, Z.: INDELible: a flexible simulator of biological sequence evolution. Molecular Biology and Evolution 26(8), 1879--1888 (2009)
4. Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
5. Generating samples under a Wright-Fisher neutral model of genetic variation