# design.file for statistical analysis **URL:** \ **Category:** Commands in mothur\ **Created:** [August 8, 2016, 7:46am UTC](https://forum.mothur.org/t/design-file-for-statistical-analysis/2944 "2016-08-08T07:46:07Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![kristinvh](https://avatars.discourse-cdn.com/v4/letter/k/d07c76/32.png) [@kristinvh](https://forum.mothur.org/u/kristinvh)\ **Post date:** [August 8, 2016, 7:46am UTC](https://forum.mothur.org/t/design-file-for-statistical-analysis/2944/1 "2016-08-08T07:46:07Z")
Hello I am using mothur for my 16S rRNA data. I have several groups I want to compare statistically, however, the “mouse.time.design” in MiSeq SOP only compare two groups (Early vs. Late). I have tried to add more groups, but it does not work. It must be possible to add more than 2 groups in the design.file? It would be very helpful to see an example of a design.file in which several groups are included. Thank you very much! ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [August 9, 2016, 10:29am UTC](https://forum.mothur.org/t/design-file-for-statistical-analysis/2944/2 "2016-08-09T10:29:24Z")
You would change the “Early” and “Late” to the names of the groups you are interested in. Can you post your design file and the error you are getting? Pat ---
**Author:** ![kristinvh](https://avatars.discourse-cdn.com/v4/letter/k/d07c76/32.png) [@kristinvh](https://forum.mothur.org/u/kristinvh)\ **Post date:** [August 9, 2016, 2:42pm UTC](https://forum.mothur.org/t/design-file-for-statistical-analysis/2944/3 "2016-08-09T14:42:26Z")
Great, thank you! It works fine when the groups are the same in both of these files “design.file” and “stability.an.thetayc.0.03.lt.ave.tre”. However, if I only want to include a subset of the groups from the file “stability.an.thtay…”, should I choose another size here: mothur \> sub.sample(shared=stability.an.shared, size=2241), or should I make another “stability.file” and run all the steps from the beginning? It is perhaps a way of specifying the groups to be used from the file “stability.an…” when I use this command: parsimony(tree=stability.an.thetayc.0.03.lt.ave.tre, group=mouse.time.design, groups=all)? I tried to specify the groups in groups=cDNA10-cDNA11-cDNA12-cDNA13, but this does not work. my design file is shown here: group sample\_type cDNA10 mucosa\_active\_bacteria cDNA11 mucosa\_active\_bacteria cDNA12 mucosa\_active\_bacteria cDNA13 mucosa\_active\_bacteria cDNA14 mucosa\_active\_bacteria cDNA15 mucosa\_active\_bacteria cDNA16 mucosa\_active\_bacteria cDNA17 mucosa\_active\_bacteria cDNA18 mucosa\_active\_bacteria cDNA19 mucosa\_active\_bacteria cDNA1 mucosa\_active\_bacteria cDNA20 mucosa\_active\_bacteria cDNA21 mucosa\_active\_bacteria cDNA22 mucosa\_active\_bacteria cDNA23 mucosa\_active\_bacteria cDNA24 mucosa\_active\_bacteria cDNA25 mucosa\_active\_bacteria cDNA27 mucosa\_active\_bacteria cDNA2 mucosa\_active\_bacteria cDNA42 mucosa\_active\_bacteria cDNA5 mucosa\_active\_bacteria cDNA6 mucosa\_active\_bacteria cDNA7 mucosa\_active\_bacteria cDNA8 mucosa\_active\_bacteria fDNA10 faeces fDNA11 faeces fDNA12 faeces fDNA13 faeces fDNA14 faeces fDNA15 faeces fDNA16 faeces fDNA17 faeces fDNA18 faeces fDNA19 faeces fDNA1 faeces fDNA20 faeces fDNA21 faeces fDNA22 faeces fDNA23 faeces fDNA24 faeces fDNA25 faeces fDNA26 faeces fDNA27 faeces fDNA28 faeces fDNA29 faeces fDNA2 faeces fDNA30 faeces fDNA31 faeces fDNA3 faeces fDNA4 faeces fDNA5 faeces fDNA6 faeces fDNA7 faeces fDNA8 faeces fDNA9 faeces mDNA10 mucosa mDNA11 mucosa mDNA12 mucosa mDNA13 mucosa mDNA14 mucosa mDNA15 mucosa mDNA16 mucosa mDNA17 mucosa mDNA18 mucosa mDNA19 mucosa mDNA1 mucosa mDNA20 mucosa mDNA21 mucosa mDNA22 mucosa mDNA23 mucosa mDNA24 mucosa mDNA25 mucosa mDNA27 mucosa mDNA2 mucosa mDNA42 mucosa mDNA5 mucosa mDNA6 mucosa mDNA7 mucosa mDNA8 mucosa Thank you 🙂 ---
**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\ **Post date:** [August 11, 2016, 4:19pm UTC](https://forum.mothur.org/t/design-file-for-statistical-analysis/2944/4 "2016-08-11T16:19:52Z")
The groups parameter in the parsimony command is used to select items from the second column of the group or design file. If you would like to select of remove groups from your files you can uses the get.groups and remove.groups commands. [http://www.mothur.org/wiki/Get.groups](http://www.mothur.org/wiki/Get.groups)[http://www.mothur.org/wiki/Remove.groups](http://www.mothur.org/wiki/Remove.groups) ---
**Author:** ![kristinvh](https://avatars.discourse-cdn.com/v4/letter/k/d07c76/32.png) [@kristinvh](https://forum.mothur.org/u/kristinvh)\ **Post date:** [August 12, 2016, 3:48pm UTC](https://forum.mothur.org/t/design-file-for-statistical-analysis/2944/5 "2016-08-12T15:48:43Z")
Great, that was very helpful, thank you very much 🙂