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Paralogy frequency (PF) calculates the number of paralogs for a OTU divided by the number of alignments that said OTU is present in. This data is saved to a CSV file called `otu_stats.csv` and, if [Matplotlib](https://matplotlib.org/) is installed, a PF plot will be saved to `paralogy_freq_plot.png`, similar to the plot in.
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![paralog_freq](uploads/763e12079f9f9c35138b746b3de92d87/paralog_freq.png)
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**Figure.** Paralogy Frequency Plot. |
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**Figure 3.** Paralogy Frequency Plot.
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## Occupancy <a name="occupancy"></a>
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A heatmap of the amount of bases present per OTU and gene partition is stored into the file `occupancy_matrix.png`. The user can choose to remove partitions and or OTUs with less than a certain amount of occupancy through the flags `--min-gene-occupancy` and `--min-otu-occupancy`. Gene partitions and OTUs which were removed via these filters are shown in red within this heatmap. |
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