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Liu K, Warnow TJ, Holder MT, Nelesen S, Yu J, Stamatakis A, Linder RC.  2012.  SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees. Systematic Biology. 61(1):90-106.
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The Holder Lab is part of the Department of Ecology and Evolutionary Biology at KU