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used new line break for docs
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JLSteenwyk committed Dec 18, 2023
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7 changes: 6 additions & 1 deletion docs/usage/index.rst
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Expand Up @@ -87,7 +87,7 @@ To report inparalogs and specify which was kept per SNAP-OG, use the -rih, \-\-r
argument. The resulting file, which will have the suffix ".inparalog_report.txt," will have three columns: |br|
- col 1 is the orthogroup file |br|
- col 2 is the inparalog that was kept |br|
- col 3 is/are the inparalog/s that were trimmed separated by a semi-colon ";" |br|
- col 3 is/are the inparalog/s that were trimmed separated by a semi-colon ";"

To generate this file, use the following command:

Expand Down Expand Up @@ -125,3 +125,8 @@ All options
+-------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
*For genome-scale analyses, we recommend changing the -o/\-\-occupancy parameter to be the same for all large gene families so that the minimum SNAP-OG occupancy is the same
for all SNAP-OGs.


.. |br| raw:: html

<br/>

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