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By default sequence data is kept on a single line. For a more readable output, you can wrap sequences at column `n` by typing `--wrap n`, where `n` is a positive integer. For example, wrap sequence data at column 80 by typing `--wrap 80`. Output alignments use the same name as the input alignments, but with the string `_pruned` appended to the end. Note that for some paralogy pruning algorithms, such as maximum inclusion (MI), multiple orthologs may be produced for a single input file and in those cases an index will also be added to the end of the name.
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![no_wrap](uploads/12a2d335a918c53ad5a5b660a03a4791/no_wrap.png)
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_sequence data on a single line (not all sequence data is visible in the pager)_
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**fig 1.**: _sequence data on a single line (not all sequence data is visible in the pager)_
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![wrap_80](uploads/124c235593ea13d8181fe33f4b1841c0/wrap_80.png)
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_sequence data wrapped at column 80, using the flag `--wrap` with the argument `80`_
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**fig 2.**: _sequence data wrapped at column 80, using the flag `--wrap` with the argument `80`_
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Summary statistics for all output alignments is saved to the file `<timestamp>_ppp_summary.csv`, where `<timestamp>` is in the following format: `year-month-date`. All CSV files uses a semicolon, `;`, as a field separator.
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![summary](uploads/eb8cca2cbfca4e0f271e8b74a72dd89d/summary.png)
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_viewing the `summary`-file using column_
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**fig 3.**: _viewing the `summary`-file using column_
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Statistics for each _individual_ output alignment is stored in the file called
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`<timestamp>_ppp_orthologs.csv`
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![ortho_stats](uploads/9bf0eda5392311a023b8b1cda5df6afe/ortho_stats.png)
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_viewing the `ortho_stats`-file using column_
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**fig 4.**: _viewing the `ortho_stats`-file using column_
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A CSV depicting the paralogy frequency will be stored in the file called
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`<timestamp>_ppp_paralog_freq.csv`. If [Matplotlib](https://matplotlib.org/) is installed, then a plot will
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