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Log-likelihood parameter of molecular clock test.
The molecular clock test was performed to gain further insight into the relative timing of duplication and divergence events.
The strict molecular clock test was performed as described in the manual, however the number of generations was increased to 2,000,000.
Previously, a molecular clock test was performed with PAUP* version 4.0b10 [ 35] by estimating the likelihood of the PhyML topology with and without forcing a molecular clock.
Each of the 25,955 genomic segments was subjected to a molecular clock test using a likelihood ratio test (LRT) with a significance level of 5% (Felsenstein 1988).
Maximum likelihood (ML) tree of AGOs showing the approximate relative time of divergence of all the nodes using the molecular clock test on 'plant AGO dataset II'.
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Despite these differences, molecular clock tests did not reject clock-like evolution for any ML analyses.
A series of molecular clock tests supported these observations.
Molecular clock tests for these trees were performed using the programs Kitsch and Fitch in PHYLIP (Felsenstein 2010).
Since the KN is the number of nonsynonymous substitutions at the non-PBR, we performed molecular clock tests for the substitutions.
The hypothesis of homogeneous rate within alignment of 16S and cyt b genes respectively was not rejected by the molecular clock tests.
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