Dear Forum,
I have a data set bacterial 16S rRNA Sanger seqs from DGGE. I have 4 samples sampled every month for a year. I only have 62 unique sequences (DGGE bands) but they occur throughout the different months (in total they occur 577 times for the 4 samples over the year). Since I only have presence-absence data I feel a bit restricted in what I can do. I have used mothur for doing part of the sequence analysis. I haven’t worked with these kinda sequences before, so I wonder if the below scripts are appropriate for these kinds of seqs…?
align.seqs(candidate=abrecovery.fasta, template=core_set_aligned.imputed.fasta, align=needleman, search=kmer)
mothur > dist.seqs(fasta=abrecovery.align, output=lt)
mothur > clearcut(phylip=abrecovery.phylip.dist)
cluster(phylip=all12month.phylip.dist)
make.shared(list=abrecovery.phylip.an.list, group=months.groups)
make.shared(list=abrecovery.phylip.an.list, group=speciestype.groups)
heatmap.sim(shared=abrecovery.phylip.an.shared, calc=braycurtis, groups=jan-feb-mar-apr-may-jun-jul-aug-sep-aug-sep-oct-nov-dec)
unifrac.unweighted(tree=abrecovery.phylip.tre, group=months.groups, random=t, distance=lt)
pcoa(phylip=abrecovery.phylip.tre1.unweighted.phylip.dist)
Sincerely,
Johannes