I have made some updates so that the MAFFT alignment module is possible to use with version 6 of MAFFT.
When looking at the code it looks like it doesn't set anything when you change method for version 4. I suggest that non-v6 code should be removed from the module. I have not done that here though, but I can if you think it's a good idea.
Updated Bio::Tools::Run::Alignment::MAFFT to work with version 6 of
I think removing v4 is a good idea, but we should poll users to see if anyone is still using v4 actively.
I can send an email to the bioperl list. The module should probably not be used with version 4 anyway since it can give the user a false impression that it's possible to choose alignment method. Changing method for version 4 doesn't change anything currently (apart from the number of cycles for two of methods).