Commands in mothur

Classify.otu results in many sequences not in the taxonomy file (4)
aligning fungal ITS sequences for pre.cluster? (2)
rename.seqs problem (1)
aligning sequences to SILVA bacterial reference database (2)
screen.seqs command hangs (3)
Compare models for AMOVA (2)
new make.contigs (4)
Generate fasta file from sub.sample shared file (3)
how to get mothur to read files from a portable hard drive (2)
ITS reference alignment (4)
non-sequence data (2)
make.contigs for dual-index with heterogeneity spacers? (2)
make.file and make.contigs " (2)" in fastq file names (2)
clearcut: any way to reassign names of tree tips? (5)
error message in pcr.seqs using new silva version 132 reference file (3)
Is there way to subsample multiple times? (3)
Curate Silva database- add sequences (2)
getting a groups file for PacBio reads (3)
make.contigs 1 sample sequenced on multiple runs (3)
Error reading in fasta file from alignseqs (1)
Clearcut: Detected 10 [ERROR] messages, please review (3)
Groups for fastq files (7)
cluster.split (4)
subsample? normalize? relabund? (2)
make.contigs and 'clean' data (2)
classify (5)
make.contigs report: overlap start and end (2)
chimera.vsearch log (2)
Error with screen.seqs after alignment (4)
get.oturep taking too long... (2)