Move MAFFT and FastTree config into config.json

[dilema]

Hello,

I thought it would be better to have the configuration of MAFFT and FastTree into the config.json file for the following reasons :

• Consistent with the documentation about configuration
• Easier to find
• Easier to modify the specific command for these two programs

Maybe it was in program_caller.py because they are default methods for MSA so you want them to be present so it wouldn't break ? But it is not the case for DIAMOND and MCL which are also default methods. So there may be another reason ?

Also, it might be good to make the FASTME command call more visible. Sorry, I'm obsessed with what parameters are used at which time.

Cheers,
dilema

P.S. : Thanks for the awesome tool and especially the last update with HOG, I was trying to do it manually. You saved me so much time !

[dilema]

I forgot to mention that it also adds a nice example for the "cmd_line_fast" option.

I saw that calling -S blast uses a specific command for blastp which is described in GetOrderedSearchCommands inside __main__.py. And actually the command is exactly the same than when calling -S blast_gz which is define in the config.json.

Does this mean that your intent when someone wanted to try different commands for the same program was that the person would create different entry and call the one they want ? Like having different sets of command for DIAMOND named differently in the json such as "diamond_1" and "diamond_2" so the person would call orthofinder -S diamond_2 depending on which set of parameters the person want ?