steineggerlab / foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.
https://foldseek.com
GNU General Public License v3.0
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Possible docs typos #293

Open calebthomas259 opened 1 week ago

calebthomas259 commented 1 week ago

Hi, thanks for the amazing software!

Just a heads up. When I type foldseek cluster into the command line (version 9.427df8a), it says the default E-value is 0.01:

 -e DOUBLE                      List matches below this E-value (range 0.0-inf) [1.000E-02]

When I type foldseek easy-cluster into the command line, I get a default value 10:

-e DOUBLE                      List matches below this E-value (range 0.0-inf) [1.000E+01]

But in the readme.md cluster options, it says the default value is 0.001, which matches neither of the previous:

-e    Sensitivity    List matches below this E-value (range 0.0-inf, default: 0.001); increasing it reports more distant structures

There seem to be similar discrepancies for foldseek search/foldseek easy-search.

Cheers!