The write.paper command will take in your original dataset and run all of the various commands on the data. Using our latest and greatest text parsing algorithms in combination with either a specified manuscript or a minimum impact factor the command will produce a submission-ready manuscript complete with figures and interpretation. When you’ve given up (or haven’t started trying) to make sense of your poorly designed experiment, run this command instead of emailing us to interpret your P-values. This command will do it all: sequence curation, combine data from different variable regions and sequencing platforms, read your mind (or your PIs mind), run alpha, beta, and population-based analyses, and even write the manuscript for you.

Default settings

By default the command will process your sff files into a manuscript to be submitted to Nature (go big or go home). This requires the basic command call:

mothur > write.paper(sff=04FOOLS01.sff)



this gives the name of the sff file you are processing

mothur > write.paper(sff=04FOOLS01.sff)


the name of your fastq files

mothur > write.paper(fastq=04FOOLS01.fastq)


The impact parameter will pick a journal format that has an impact factor closest to your score of choice

mothur > write.paper(sff=04FOOLS01.sff, impact=11)


The journal option will pick your desired journal of choice

mothur > write.paper(sff=04FOOLS01.sff, journal=Biotechniques)