- * -t : file-name for output table of all vs. all ortholgy support
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- * -q : name for query (sequence/node), if this is used, `[`outfile`]` is required as well
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- * -s : sort (default: 2)
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- * -u : to output ultra-paralogs (species specific expansions/paralogs)
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- * -cu: cutoff for ultra-paralog output (default: 50)
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-==== Note ====
-
-Either output of all vs. all ortholgy support with -t=`<`output table`>` and/or output for one query sequence with -q and a `[`outfile`]` are required.
-
-==== Sort ====
-
- * 0: orthologies
- * 1: orthologies > super orthologies
- * 2: super orthologies > orthologies
-