Author Name: Adam Retchless (Adam Retchless)
Original Redmine Issue: 3201, https://redmine.open-bio.org/issues/3201
Original Date: 2011-04-13
Original Assignee: Bioperl Guts

The documentation for the Phyml wrapper does not describe how to send Phyml instructions for the calculation of bootstrap values or other confidence values.

The “_setparams” subroutine has a comment line explicitly stating “no bootstrap sets”, and cannot write this parameter (-b or —bootstrap in phyml 3).

If adding this parameter is not trivial, it may be worthwhile to clearly document that this feature is not implemented in the wrapper, since these confidence values are an important part of phylogeny estimation.