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. 2010 Mar 10;5(3):e9490. doi: 10.1371/journal.pone.0009490

Table 2. Average log-likelihood for genuine alignments with 500 sequences.

Method 16S COG
RAxML 7.0.4 (GTR+CAT or JTT+CAT, SPRs) −168,104 −206,724
FastTree 2.0.0 (GTR+CAT or JTT+CAT) −168,577 −206,993
PhyML 3.0 (GTR+Inline graphic or JTT+Inline graphic, no SPRs) −168,603 −207,156

For all topologies, the log likelihood was computed with RAxML 7, re-optimized branch lengths and model parameters, and the GTR+Inline graphic or JTT+Inline graphic models for 16S or COG, respectively. All differences between FastTree and other methods were statistically significant (Inline graphic) except for the comparison with PhyML on 16S rRNAs (Inline graphic, paired Inline graphic test).