Hi, reading the posts made me realize I have a basic question, but I can´t find an answer by myself. I need to analyze how different two samples are. I have the .dist with all the sequences from both libraries but I do not know how to generate the groupfile that is also needed (is it a FASTA format with all the sequences instead of PHYLIP?).
Thanks for your help. Kind regards
If this is 454/MiSeq data then you would use the group file that is generated in trim.seqs/make.contigs.
If this is Sanger data, then you’ll need to make the group file yourself. THe first column would be the sequence name and the second would be the group that it belongs to. There’s an example of how to do thin in the Sogin and Esophagus analysis example pages on the wiki.
Thank you very much for your response. I have already done this, and saved the file as .txt but an error occurs because the window closes after this:
read.dist(phylip=1.dist,group=a.txt) I believe the problem is the .txt that is not recognized, but I do not know which option should be friendly for mothur.
Thanks again
What is the size of 1.dist and is it a column formatted matrix or a phylip formatted matrix? It should be phylip formatted.
1.dist is a matrix obtained in phylip and its size is small, 51 sequences from two groups.
Thank you very much.
What version of mothur are you using? I ask because the read.dist command is not part of our current version, 1.31. Here is a link to our download page, http://www.wiki.mothur.org/wiki/Download_mothur and group file page, http://www.wiki.mothur.org/wiki/Group_file. If you are still having trouble you can send your input files to mothur.bugs@gmail.com and I will take a look.