diff --git a/docs/usage/index.rst b/docs/usage/index.rst index 084576d8..5eaa45f8 100644 --- a/docs/usage/index.rst +++ b/docs/usage/index.rst @@ -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: @@ -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 + +