How to make a group file

Commands in mothur
1

I am interested to use Libshuff command and Venn command in Mothur.

I have a few questions which I can’t figure out by myself after reading through out the mother wiki.

I have 3 different samples, each samples contained around 100 sequences.
I tried to make a group file by using command make.group:
mothur > make.group(fasta=Sample1.fasta-Sample2.fasta-Sample3.fasta, group=A-B-C)

And I got groups file from that.

(A) But, how to combine fasta file from all these three Sample? I would like to have fasta file for combination of Sample1,Sample2 and Sample3.

  1. For libshuff command,
    mothur > libshuff(phylip=98_lt_phylip_amazon.dist, group=amazon.groups)
    I need to have phylip file.dist and group file.

Previously, in order to get .dist file, I used dist.seqs command which lead to column-formatted distance matrix.

(B) May I know how to creat .dist file to phylip-formatted distance matrix?


I'm confused how to make group and share file for all my 3 samples.

I hope I can get help from here.

Thank you so much

2
  1. To do it within mothur, you can use the merge.files command:

merge.files(input=Sample1.fasta-Sample2.fasta-Sample3.fasta, output=allreads.fasta)

  1. To get a phylip-formatted distance matrix use the dist.seqs command with the lower triangle (lt) parameter:

dist.seqs(fasta=final.fasta, output=lt)

I hope that helps.

3

Thank you so much for your help.

I managed to combine all three group in one fasta and can make phylip formatted distance matrix file.

As I mentioned before, I already make.group for Sample1, Sample2 and Sample3 in one groups file = ALL.groups.

So, when I tried to use libshuff command,

mothur > libshuff(phylips=ALLREADS.filter.phylip.dist, group=ALL.groups)

It said cannot open the ALL.groups file.

Can I know why? How to make the groups file can be open?

I’m sorry coz confuse about this.

Thank you again

4

http://www.mothur.org/wiki/Frequently_asked_questions#Mothur_can.27t_find_my_input_files

5

Thank you! :smiley: