Additional file 7: Figure S6.
RAxML performs similarly regardless of whether it is given a fixed reference tree. Despite the more restricted optimization landscape offered by a fixed reference tree, in our simulations, there was little detectible difference in performance. Here, data for the 16S rRNA gene family are shown. We plot the mean nRF (left) and mean DF quartiles for simulations with 200 reads (right), over 30 simulations for each combination of simulation parameters. Vertical error bars show a standard deviation above and below the mean.
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Riesenfeld and Pollard BMC Genomics 2013 14:419 doi:10.1186/1471-2164-14-419