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Support values were largely similar between the two partitioning approaches.
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That the communities appear to correspond well to periods indicate the existence of correlation between the two partitions.
First, a Fisher's exact test compared p between the two partitions.
There are striking similarities between the two partitions.
The agreement between the two partitions was then evaluated using the adjusted Rand index [ 33].
If one were interested in differentiating between the two partitions, experiment 2 would be much preferable.
However, there are also several qualitative differences between the two partitions.
In fact, when τ = 0.5, the difference of evolutionary rates between the two partitions is already three-fold.
Significant discrepancies between the two partitions of the window are calculated based on the difference in the number of variable sites (VI) on either sides of the central partition.
We varied τ from 0 (no heterotachy, homogeneous evolutionary rate) to 0.9 (high level of heterotachy, the evolutionary rate differing by a factor of 19 between the two partitions).
The NMI index varies between one, when the two partitions are equal, and zero, when the two classifications are completely disjoined.
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