Restrict Model types

[GoogleCodeExporter]

Is there a way to restrict the models included in a run? I tried the "-MtArt? F 
–MtREV F –MtMam? F" format from the old version and it doesn't seem to 
work. Thanks, Sarah

Original issue reported on code.google.com by sarilo...@gmail.com on 16 Jul 2013 at 4:19

[GoogleCodeExporter]

On one hand you can restrict the matrices that way:

 -[matrix]
            Include matrix (Amino-acid) = JTT LG DCMut MtREV MtMam MtArt Dayhoff WAG 
                                      RtREV CpREV Blosum62 VT HIVb HIVw FLU 

e.g., -MtArt -MtREV -MtMam

On the other hand, you can choose if you want to use both empirical and 
model-driven frequencies with -F argument, but you cannot use different 
frequencies/rate variation parameters for each single matrix.

In your case you shoud use "-MtArt -MtREV -MtMam -F"

I hope this is what you need.

Original comment by DiegoDL84 on 16 Jul 2013 at 4:27

• Changed state: Done
• Added labels: Type-Other, Component-UI, Usability
• Removed labels: Type-Defect, Priority-Medium

[GoogleCodeExporter]

BTW, please use the discussion forum for further questions:

https://groups.google.com/forum/m/#!forum/prottest

Original comment by DiegoDL84 on 16 Jul 2013 at 4:28