Phylogenetic Tree

Commands in mothur
1

Hello mothur’s users!

I followed the MiSeq SOP pipeline of mothur in order to preprocess and assign taxonomy using 16S rDNA amplicons data.

When I tried to go further, after I had got my OTU table, I couldn’t do the phylogenetic tree using the “clearcut” command because give me the following error:

clearcut(phylip=nice15.trim.contigs.good.unique.good.filter.unique.precluster.pick.phylip.dist)

Clearcut: Memory allocation error in NJ_parse_distance_matrix()
Clearcut: Syntax error in distance matrix at offset 7.

I didn’t understand this error.
Can anyone help me on this, please!

Thanks in advance!
Best wishes,
@renh@

2

Your distance matrix is probably too large. I’d suggest sticking with OTU and phylotyping methods. I have yet to see a Unifrac or Phylogenetic diversity analysis that disagreed with a OTU-based analysis.

Pat

3

Thank you Pat,
@renh@