Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By C. Randal Linder, Kevin Liu, Serita Nelesen, Sindhu Raghavan, Tandy Warnow
Issue Date:January 2009
Several methods have been developed for simultaneous estimation of alignment and tree, of which POY is the most popular. In a 2007 paper published in Systematic Biology, Ogden and Rosenberg reported on a simulation study in which they compared POY to estim...