when i learning how to use MOTHUR according to Analysis exampkes about “Esophageal community analysis”, i met some problems about the command dist.seqs.
THE link is http://www.mothur.org/wiki/Esophageal_community_analysis
After i typed the commands following the example:mothur > dist.seqs(fasta=esophagus.good.filter.fasta, phylip=T), the software said that phylip is not a valid parameter. So the command stopped.
What i should use this command correctly to run some of the hypothesis testing procedures and generate a phylip-formatted distance matrix like what mentioned on this web.
Thank you .