Phylogenetic tree error with dist.seqs

Commands in mothur
1

I am having some trouble generating a Phylogenetic tree. I believe all of my other steps have been correct up to this point, and the error I’m getting doesn’t seem to suggest I’ve done something wrong elsewhere. It almost seems like my version of mothur may be wrong since an output type for dist.seqs just seems to be missing.

I used:

sudo apt-get install mothur

to install mothur. Which installed mothur v.1.24.1 Last updated: 3/16/2012. This has worked for everything else, but something seems off here. Here’s the command I’m running and the error message I receive.

dist.seqs(fasta=control.final.fasta, output=phylip, processors=4)

phylip is not a valid output form. Options are column, lt and square. I will use column.
0 0
100 0
600 0
200 1
500 1
300 1
800 1
811 1
573 1
700 1
702 1
400 1
405 1

Output File Name:
control.final.dist

It took 2 to calculate the distances for 812 sequences.

Note that it also write to control.final.dist instead of control.final.phylip.dist…

2

So I fixed my own problem by updating mothur to 1.32.1. This makes me wonder if some of the other bugs I’ve been hitting along the way have been caused by the same old version.

I Guess more importantly to anyone using mothur on linux, DON’T USE:

sudo apt-get install mothur