I am a new user of Mothur and trying to do analysis of my 454 data (functional gene). A have generated an ARB database for my functional gene with few basic meta information. I am now interested to do phylotype (taxonomy) based analysis, but dont know how to make a taxonomy file. Any instruction in this regard is very much appreciated.
The taxonomy file for mothur is a 2 column tab delimited file. The taxonomy levels are separated by semicolons.
If you are new to mothur, you may want to check out Pat’s example analysis, http://www.mothur.org/wiki/Schloss_SOP.
MOTHUR is a good comprehensive tools for phylogenetic analysis, however has several limitations for functional genes (e.g. amoA, nirK, nosZ, mcrA, etc).
For example, you will be unable to align, classify your sequences into taxonomic groups, chimera, among other commands (unless you create a database specifically for a particular functional group, this topic have been extensively discuss before at this forum).
But you can perform a lot of analysis. First align the sequences of each functional group using a stand alone alignment software (e.g. ClustalX). Once you have you alignment you can import the alignment into MOTHUR (as FASTA file) and generate a distance matrices. Once you create a share file you can perform any alpha and beta diversity and even hypothesis driven analysis.
Just remember the cutoff value used for OTU identification could vary by functional gene and may be not the same as the one used for 16S rRNA gene.
Hope this help.
Thanks very much regarding the info. on Taxonomy file and working with mothur for the functional gene.