Same file for candidate and template? read.dist crashes?

Commands in mothur
1

I have a file of non 16S sequences. There is not a template file for my sequences so I was just going to use the same fasta file as the candidate and template. Will this work? The sequences may or may not be similar to each other. All I want to do is cluster them into like groups. In order to do this I thought I needed to run align.seqs then filter.seqs then dist.seqs then read.dist and finally cluster. However, when I press enter after the read.dist(phylip=…dist) command, the operation completely closes. Can you tell me what may be happening?

Attached is a copy of the .dist file.

2

Yeah, this won’t work. align.seqs assumes that the template file is already aligned. There are a few options…

  1. You could generate a multiple sequence alignment using something like muscle or clustal, export the alignment in fasta format and then proceed to the steps following align.seqs, without actually doing align.seqs.

  2. You could use pairwise.seqs (http://www.mothur.org/wiki/Pairwise.seqs) to calculate distances between sequences. Then with the outputted distance matrix you can then proceed to cluster.

Hope this helps…
Pat